1
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Asthana A, Corona A, Shin WJ, Kwak MJ, Gaughan C, Tramontano E, Jung JU, Schobert R, Jha BK, Silverman RH, Biersack B. Analogs of the Catechol Derivative Dynasore Inhibit HIV-1 Ribonuclease H, SARS-CoV-2 nsp14 Exoribonuclease, and Virus Replication. Viruses 2023; 15:1539. [PMID: 37515225 PMCID: PMC10385162 DOI: 10.3390/v15071539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Viral replication often depends on RNA maturation and degradation processes catalyzed by viral ribonucleases, which are therefore candidate targets for antiviral drugs. Here, we synthesized and studied the antiviral properties of a novel nitrocatechol compound (1c) and other analogs that are structurally related to the catechol derivative dynasore. Interestingly, compound 1c strongly inhibited two DEDD box viral ribonucleases, HIV-1 RNase H and SARS-CoV-2 nsp14 3'-to-5' exoribonuclease (ExoN). While 1c inhibited SARS-CoV-2 ExoN activity, it did not interfere with the mRNA methyltransferase activity of nsp14. In silico molecular docking placed compound 1c in the catalytic pocket of the ExoN domain of nsp14. Finally, 1c inhibited SARS-CoV-2 replication but had no toxicity to human lung adenocarcinoma cells. Given its simple chemical synthesis from easily available starting materials, these results suggest that 1c might be a lead compound for the design of new antiviral compounds that target coronavirus nsp14 ExoN and other viral ribonucleases.
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Affiliation(s)
- Abhishek Asthana
- Cancer Biology, Lerner Research Institute, Cleveland Clinic, 2111 East 96th St, Cleveland, OH 44106, USA
| | - Angela Corona
- Laboratorio di Virologia Molecolare, Dipartimento di Scienze della Vita e Dell'Ambiente, Universitá degli Studi di Cagliari, Cittadella Universitaria di Monserrato SS554, 09042 Monserrato, Italy
| | - Woo-Jin Shin
- Cancer Biology, Lerner Research Institute, Cleveland Clinic, 2111 East 96th St, Cleveland, OH 44106, USA
| | - Mi-Jeong Kwak
- Cancer Biology, Lerner Research Institute, Cleveland Clinic, 2111 East 96th St, Cleveland, OH 44106, USA
| | - Christina Gaughan
- Cancer Biology, Lerner Research Institute, Cleveland Clinic, 2111 East 96th St, Cleveland, OH 44106, USA
| | - Enzo Tramontano
- Laboratorio di Virologia Molecolare, Dipartimento di Scienze della Vita e Dell'Ambiente, Universitá degli Studi di Cagliari, Cittadella Universitaria di Monserrato SS554, 09042 Monserrato, Italy
| | - Jae U Jung
- Cancer Biology, Lerner Research Institute, Cleveland Clinic, 2111 East 96th St, Cleveland, OH 44106, USA
| | - Rainer Schobert
- Organic Chemistry 1, University of Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
| | - Babal Kant Jha
- Center for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute and Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 2111 East 96th St, Cleveland, OH 44195, USA
| | - Robert H Silverman
- Cancer Biology, Lerner Research Institute, Cleveland Clinic, 2111 East 96th St, Cleveland, OH 44106, USA
| | - Bernhard Biersack
- Organic Chemistry 1, University of Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
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2
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Al Nasr IS, Corona A, Koko WS, Khan TA, Ben Said R, Daoud I, Rahali S, Tramontano E, Schobert R, Amdouni N, Biersack B. Versatile anti-infective properties of pyrido- and dihydropyrido[2,3-d]pyrimidine-based compounds. Bioorg Med Chem 2023; 90:117376. [PMID: 37336083 DOI: 10.1016/j.bmc.2023.117376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/16/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023]
Abstract
A series of 1H-indeno[2',1':5,6]dihydropyrido[2,3-d]pyrimidine and 1H-indeno[2',1':5,6]pyrido[2,3-d]pyrimidine derivatives was prepared and screened for antiparasitic and viral RNase H inhibitory activity. Several compounds showed considerable activity against Toxoplasma gondii parasites and Leishmania major amastigotes, which warrants further investigation. Based on the structural similarities of certain derivatives with common viral RNase H inhibitors, a HIV-1 RNase H assay was used to study the RNase H inhibition by selected test compounds. Docking of active derivatives into the active site of the HIV-1 RNase H enzyme was carried out. The new compound 2a, inactive in the antiparasitic tests, showed distinct HIV-1 RNase H inhibition. Thus, ring substitution determines antiparasitic or HIV-1 RNase H inhibitory activity of this promising compound class.
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Affiliation(s)
- Ibrahim S Al Nasr
- Department of Biology, College of Science and Arts, Qassim University, Unaizah 51911, Saudi Arabia; Department of Science Laboratories, College of Science and Arts, Qassim University, Ar Rass 51921, Saudi Arabia
| | - Angela Corona
- Laboratorio di Virologia Molecolare, Dipartimento di Scienze della Vita e Dell'Ambiente, Universitá degli Studi di Cagliari, Cittadella Universitaria di Monserrato SS554, 09042 Monserrato, Italy
| | - Waleed S Koko
- Department of Science Laboratories, College of Science and Arts, Qassim University, Ar Rass 51921, Saudi Arabia
| | - Tariq A Khan
- Department of Clinical Nutrition, College of Applied Health Sciences, Qassim University, Ar Rass 51921, Saudi Arabia
| | - Ridha Ben Said
- Laboratoire de Caractérisations, Applications et Modélisations des Matériaux, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis, Tunisia; Department of Chemistry, College of Science and Arts at Ar Rass, Qassim University, Ar Rass 51921, Saudi Arabia
| | - Ismail Daoud
- University Mohamed Khider, Department of Matter Sciences, BP 145 RP, Biskra, Algeria; Laboratory of Natural and Bio-active Substances, Faculty of Science, Tlemcen University, P.O. Box 119, Tlemcen, Algeria
| | - Seyfeddine Rahali
- Department of Chemistry, College of Science and Arts at Ar Rass, Qassim University, Ar Rass 51921, Saudi Arabia
| | - Enzo Tramontano
- Laboratorio di Virologia Molecolare, Dipartimento di Scienze della Vita e Dell'Ambiente, Universitá degli Studi di Cagliari, Cittadella Universitaria di Monserrato SS554, 09042 Monserrato, Italy
| | - Rainer Schobert
- Organische Chemie I, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany
| | - Noureddine Amdouni
- Laboratoire de Caractérisations, Applications et Modélisations des Matériaux, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Bernhard Biersack
- Organische Chemie I, Universität Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany.
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3
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Rugemalila J, Kamori D, Kunambi P, Mizinduko M, Sabasaba A, Masoud S, Msafiri F, Mugusi S, Mutagonda R, Mlunde L, Amani D, Mboya E, Mahiti M, Ruhago G, Mushi J, Sambu V, Mgomella G, Jullu B, Maokola W, Njau P, Mutayoba B, Barabona G, Ueno T, Pembe A, Nagu T, Sunguya B, Aboud S. HIV virologic response, patterns of drug resistance mutations and correlates among adolescents and young adults: A cross-sectional study in Tanzania. PLoS One 2023; 18:e0281528. [PMID: 36821538 PMCID: PMC9949668 DOI: 10.1371/journal.pone.0281528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/25/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND The emergence of HIV drug resistance mutations (DRMs) is of significant threat to achieving viral suppression (VS) in the quest to achieve global elimination targets. We hereby report virologic outcomes and patterns of acquired DRMs and its associated factors among adolescents and young adults (AYA) from a broader HIV drug resistance surveillance conducted in Tanzania. METHODS Data of AYA was extracted from a cross-sectional study conducted in 36 selected facilities using a two-stage cluster sampling design. Dried blood spot (DBS) samples were collected and samples with a viral load (VL) ≥1000 copies/mL underwent genotyping for the HIV-1 pol gene. Stanford HIV database algorithm predicted acquired DRMs, Fisher's exact test and multivariable logistic regression assessed factors associated with DRMs and VS, respectively. FINDINGS We analyzed data of 578 AYA on antiretroviral therapy (ART) for 9-15 and ≥ 36 months; among them, 91.5% and 88.2% had VS (VL<1000copies/mL) at early and late time points, respectively. Genotyping of 64 participants (11.2%) who had VL ≥1000 copies/ml detected 71.9% of any DRM. Clinically relevant DRMs were K103N, M184V, M41L, T215Y/F, L210W/L, K70R, D67N, L89V/T, G118R, E138K, T66A, T97A and unexpectedly absent K65R. Participants on a protease inhibitor (PI) based regimen were twice as likely to not achieve VS compared to those on integrase strand transfer inhibitors (INSTI). The initial VL done 6 months after ART initiation of ≥1000copies/mL was the primary factor associated with detecting DRMs (p = .019). CONCLUSIONS VS amongst AYA is lower than the third UNAIDs target. Additionally, a high prevalence of ADR and high levels of circulating clinically relevant DRMs may compromise the long-term VS in AYA. Furthermore, the first VL result of ≥1000copies/ml after ART initiation is a significant risk factor for developing DRMs. Thus, strict VL monitoring for early identification of treatment failure and genotypic testing during any ART switch is recommended to improve treatment outcomes for AYA.
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Affiliation(s)
- Joan Rugemalila
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Internal Medicine, Muhimbili National Hospital, Dar es Salaam, Tanzania
- * E-mail:
| | - Doreen Kamori
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Peter Kunambi
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Mucho Mizinduko
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Amon Sabasaba
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Salim Masoud
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Frank Msafiri
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Sabina Mugusi
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Rita Mutagonda
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Linda Mlunde
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Davis Amani
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Erick Mboya
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Macdonald Mahiti
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - George Ruhago
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - Veryeh Sambu
- National AIDS Control Programme, Dodoma, Tanzania
| | - George Mgomella
- Centers for Disease Control and Prevention, Dar es Salaam, Tanzania
| | - Boniface Jullu
- Management and Development for Health, Dar es Salaam, Tanzania
| | | | - Prosper Njau
- National AIDS Control Programme, Dodoma, Tanzania
| | | | - Godfrey Barabona
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Takamasa Ueno
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Andrea Pembe
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Tumaini Nagu
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Bruno Sunguya
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Said Aboud
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
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4
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Fois B, Corona A, Tramontano E, Distinto S, Maccioni E, Meleddu R, Caboni P, Floris C, Cottiglia F. Flavonoids and Acid-Hydrolysis derivatives of Neo-Clerodane diterpenes from Teucrium flavum subsp. glaucum as inhibitors of the HIV-1 reverse transcriptase-associated RNase H function. J Enzyme Inhib Med Chem 2021; 36:749-757. [PMID: 33715562 PMCID: PMC7952052 DOI: 10.1080/14756366.2021.1887170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bioassay-guided fractionation of the ethyl acetate extract from Teucrium flavum subsp. glaucum, endowed with inhibitory activity towards the HIV-1 reverse transcriptase–associated RNase H function, led to the isolation of salvigenin (1), cirsimaritin (2) and cirsiliol (3) along with the neo-clerodanes teuflavin (4) and teuflavoside (5). Acid hydrolysis of the inactive teuflavoside provided three undescribed neo-clerodanes, flavuglaucins A-C (7-9) and one known neo-clerodane (10). Among all neo-clerodanes, flavuglaucin B showed the highest inhibitory activity towards RNase H function with a IC50 value of 9.1 μM. Molecular modelling and site-directed mutagenesis analysis suggested that flavuglaucin B binds into an allosteric pocket close to RNase H catalytic site. This is the first report of clerodane diterpenoids endowed with anti-reverse transcriptase activity. Neo-clerodanes represent a valid scaffold for the development of a new class of HIV-1 RNase H inhibitors.
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Affiliation(s)
- Benedetta Fois
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy.,Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Rita Meleddu
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Pierluigi Caboni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
| | - Costantino Floris
- Department of Chemical and Geological Sciences, University of Cagliari, Monserrato, Italy
| | - Filippo Cottiglia
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Italy
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5
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Meleddu R, Corona A, Distinto S, Cottiglia F, Deplano S, Sequeira L, Secci D, Onali A, Sanna E, Esposito F, Cirone I, Ortuso F, Alcaro S, Tramontano E, Mátyus P, Maccioni E. Exploring New Scaffolds for the Dual Inhibition of HIV-1 RT Polymerase and Ribonuclease Associated Functions. Molecules 2021; 26:molecules26133821. [PMID: 34201561 PMCID: PMC8270338 DOI: 10.3390/molecules26133821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/30/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
Current therapeutic protocols for the treatment of HIV infection consist of the combination of diverse anti-retroviral drugs in order to reduce the selection of resistant mutants and to allow for the use of lower doses of each single agent to reduce toxicity. However, avoiding drugs interactions and patient compliance are issues not fully accomplished so far. Pursuing on our investigation on potential anti HIV multi-target agents we have designed and synthesized a small library of biphenylhydrazo 4-arylthiazoles derivatives and evaluated to investigate the ability of the new derivatives to simultaneously inhibit both associated functions of HIV reverse transcriptase. All compounds were active towards the two functions, although at different concentrations. The substitution pattern on the biphenyl moiety appears relevant to determine the activity. In particular, compound 2-{3-[(2-{4-[4-(hydroxynitroso)phenyl]-1,3-thiazol-2-yl} hydrazin-1-ylidene) methyl]-4-methoxyphenyl} benzamide bromide (EMAC2063) was the most potent towards RNaseH (IC50 = 4.5 mM)- and RDDP (IC50 = 8.0 mM) HIV RT-associated functions.
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Affiliation(s)
- Rita Meleddu
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Filippo Cottiglia
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Serenella Deplano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Lisa Sequeira
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Daniela Secci
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Alessia Onali
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Erica Sanna
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Italo Cirone
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, Università Magna Graecia di Catanzaro, Campus ‘S. Venuta’, Viale Europa, 88100 Catanzaro, Italy; (F.O.); (S.A.)
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università Magna Graecia di Catanzaro, Campus ‘S. Venuta’, Viale Europa, 88100 Catanzaro, Italy; (F.O.); (S.A.)
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
| | - Péter Mátyus
- Institute of Digital Health Sciences, Faculty of Health and Public Services, Semmelweis University, Ferenc tér 15, 1094 Budapest, Hungary;
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, 09042 Cagliari, Italy; (R.M.); (A.C.); (S.D.); (F.C.); (S.D.); (L.S.); (D.S.); (A.O.); (E.S.); (F.E.); (I.C.); (E.T.)
- Correspondence: ; Tel.: +39-070-6758744
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6
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Messore A, Corona A, Madia VN, Saccoliti F, Tudino V, De Leo A, Ialongo D, Scipione L, De Vita D, Amendola G, Novellino E, Cosconati S, Métifiot M, Andreola ML, Esposito F, Grandi N, Tramontano E, Costi R, Di Santo R. Quinolinonyl Non-Diketo Acid Derivatives as Inhibitors of HIV-1 Ribonuclease H and Polymerase Functions of Reverse Transcriptase. J Med Chem 2021; 64:8579-8598. [PMID: 34106711 PMCID: PMC8279492 DOI: 10.1021/acs.jmedchem.1c00535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
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Novel anti-HIV agents
are still needed to overcome resistance issues,
in particular inhibitors acting against novel viral targets. The ribonuclease
H (RNase H) function of the reverse transcriptase (RT) represents
a validated and promising target, and no inhibitor has reached the
clinical pipeline yet. Here, we present rationally designed non-diketo
acid selective RNase H inhibitors (RHIs) based on the quinolinone
scaffold starting from former dual integrase (IN)/RNase H quinolinonyl
diketo acids. Several derivatives were synthesized and tested against
RNase H and viral replication and found active at micromolar concentrations.
Docking studies within the RNase H catalytic site, coupled with site-directed
mutagenesis, and Mg2+ titration experiments demonstrated
that our compounds coordinate the Mg2+ cofactor and interact
with amino acids of the RNase H domain that are highly conserved among
naïve and treatment-experienced patients. In general, the new
inhibitors influenced also the polymerase activity of RT but were
selective against RNase H vs the IN enzyme.
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Affiliation(s)
- Antonella Messore
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Valentina Noemi Madia
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Francesco Saccoliti
- D3 PharmaChemistry, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy
| | - Valeria Tudino
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Alessandro De Leo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Davide Ialongo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Luigi Scipione
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Daniela De Vita
- Department of Environmental Biology, "Sapienza" University of Rome, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Giorgio Amendola
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Ettore Novellino
- Department of Pharmacy, University Federico II of Naples, Via D. Montesano 49, 80131 Naples, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Mathieu Métifiot
- Laboratoire MFP, UMR 5234, CNRS - Université de Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux cedex, France
| | - Marie-Line Andreola
- Laboratoire MFP, UMR 5234, CNRS - Université de Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux cedex, France
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
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7
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Corona A, Seibt S, Schaller D, Schobert R, Volkamer A, Biersack B, Tramontano E. Garcinol from Garcinia indica inhibits HIV-1 reverse transcriptase-associated ribonuclease H. Arch Pharm (Weinheim) 2021; 354:e2100123. [PMID: 34008218 DOI: 10.1002/ardp.202100123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/20/2021] [Accepted: 04/23/2021] [Indexed: 11/06/2022]
Abstract
The bioactive components of Garcinia indica, garcinol (camboginol), and isogarcinol (cambogin), are suitable drug candidates for the treatment of various human diseases. HIV-1-RNase H assay was used to study the RNase H inhibition by garcinol and isogarcinol. Docking of garcinol into the active site of the enzyme was carried out to rationalize the difference in activities between the two compounds. Garcinol showed higher HIV-1-RNase H inhibition than the known inhibitor RDS1759 and retained full potency against the RNase H of a drug-resistant HIV-1 reverse transcriptase form. Isogarcinol was distinctly less active than garcinol, indicating the importance of the enolizable β-diketone moiety of garcinol for anti-RNase H activity. Docking calculations confirmed these findings and suggested this moiety to be involved in the chelation of metal ions of the active site. On the basis of its HIV-1 reverse transcriptase-associated RNase H inhibitory activity, garcinol is worth being further explored concerning its potential as a cost-effective treatment for HIV patients.
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Affiliation(s)
- Angela Corona
- Laboratorio di Virologia Molecolare, Dipartimento di Scienze della Vita e Dell'Ambiente, Universitá degli Studi di Cagliari, Monserrato, Italy
| | - Sebastian Seibt
- Organic Chemistry Laboratory, University of Bayreuth, Bayreuth, Germany
| | - David Schaller
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Rainer Schobert
- Organic Chemistry Laboratory, University of Bayreuth, Bayreuth, Germany
| | - Andrea Volkamer
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Bernhard Biersack
- Organic Chemistry Laboratory, University of Bayreuth, Bayreuth, Germany
| | - Enzo Tramontano
- Laboratorio di Virologia Molecolare, Dipartimento di Scienze della Vita e Dell'Ambiente, Universitá degli Studi di Cagliari, Monserrato, Italy.,Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
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8
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Tocco G, Esposito F, Caboni P, Laus A, Beutler JA, Wilson JA, Corona A, Le Grice SFJ, Tramontano E. Scaffold hopping and optimisation of 3',4'-dihydroxyphenyl- containing thienopyrimidinones: synthesis of quinazolinone derivatives as novel allosteric inhibitors of HIV-1 reverse transcriptase-associated ribonuclease H. J Enzyme Inhib Med Chem 2020; 35:1953-1963. [PMID: 33143469 PMCID: PMC7646544 DOI: 10.1080/14756366.2020.1835884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bioisosteric replacement and scaffold hopping are powerful strategies in drug design useful for rationally modifying a hit compound towards novel lead therapeutic agents. Recently, we reported a series of thienopyrimidinones that compromise dynamics at the p66/p51 HIV-1 reverse transcriptase (RT)-associated Ribonuclease H (RNase H) dimer interface, thereby allosterically interrupting catalysis by altering the active site geometry. Although they exhibited good submicromolar activity, the isosteric replacement of the thiophene ring, a potential toxicophore, is warranted. Thus, in this article, the most active 2-(3,4-dihydroxyphenyl)-5,6-dimethylthieno[2,3-d]pyrimidin-4(3H)-one 1 was selected as the hit scaffold and several isosteric substitutions of the thiophene ring were performed. A novel series of highly active RNase H allosteric quinazolinone inhibitors was thus obtained. To determine their target selectivity, they were tested against RT-associated RNA-dependent DNA polymerase (RDDP) and integrase (IN). Interestingly, none of the compounds were particularly active on (RDDP) but many displayed micromolar to submicromolar activity against IN.
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Affiliation(s)
- Graziella Tocco
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Cagliari, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Cagliari, Italy
| | - Pierluigi Caboni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Cagliari, Italy
| | - Antonio Laus
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Cagliari, Italy
| | - John A Beutler
- Molecular Targets Program, National Cancer Institute, Frederick, MD, USA
| | - Jennifer A Wilson
- Molecular Targets Program, National Cancer Institute, Frederick, MD, USA
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Cagliari, Italy
| | | | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Cagliari, Italy
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9
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Corona A, Ballana E, Distinto S, Rogolino D, Del Vecchio C, Carcelli M, Badia R, Riveira-Muñoz E, Esposito F, Parolin C, Esté JA, Grandi N, Tramontano E. Targeting HIV-1 RNase H: N'-(2-Hydroxy-benzylidene)-3,4,5-Trihydroxybenzoylhydrazone as Selective Inhibitor Active against NNRTIs-Resistant Variants. Viruses 2020; 12:v12070729. [PMID: 32640577 PMCID: PMC7412550 DOI: 10.3390/v12070729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/28/2020] [Accepted: 07/01/2020] [Indexed: 02/07/2023] Open
Abstract
HIV-1 infection requires life-long treatment and with 2.1 million new infections/year, faces the challenge of an increased rate of transmitted drug-resistant mutations. Therefore, a constant and timely effort is needed to identify new HIV-1 inhibitors active against drug-resistant variants. The ribonuclease H (RNase H) activity of HIV-1 reverse transcriptase (RT) is a very promising target, but to date, still lacks an efficient inhibitor. Here, we characterize the mode of action of N’-(2-hydroxy-benzylidene)-3,4,5-trihydroxybenzoylhydrazone (compound 13), an N-acylhydrazone derivative that inhibited viral replication (EC50 = 10 µM), while retaining full potency against the NNRTI-resistant double mutant K103N-Y181C virus. Time-of-addition and biochemical assays showed that compound 13 targeted the reverse-transcription step in cell-based assays and inhibited the RT-associated RNase H function, being >20-fold less potent against the RT polymerase activity. Docking calculations revealed that compound 13 binds within the RNase H domain in a position different from other selective RNase H inhibitors; site-directed mutagenesis studies revealed interactions with conserved amino acid within the RNase H domain, suggesting that compound 13 can be taken as starting point to generate a new series of more potent RNase H selective inhibitors active against circulating drug-resistant variants.
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Affiliation(s)
- Angela Corona
- Department of Life and Environmental Sciences University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (S.D.); (F.E.); (N.G.); (E.T.)
- Correspondence: ; Tel.: +39-070-6754530
| | - Ester Ballana
- AIDS Research Institute—IrsiCaixa, 08916 Badalona, Spain; (E.B.); (R.B.); (E.R.-M.); (J.A.E.)
| | - Simona Distinto
- Department of Life and Environmental Sciences University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (S.D.); (F.E.); (N.G.); (E.T.)
| | - Dominga Rogolino
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.R.); (M.C.)
| | - Claudia Del Vecchio
- Department of Molecular Medicine, University of Padova, 35122 Padova, Italy; (C.D.V.); (C.P.)
| | - Mauro Carcelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.R.); (M.C.)
| | - Roger Badia
- AIDS Research Institute—IrsiCaixa, 08916 Badalona, Spain; (E.B.); (R.B.); (E.R.-M.); (J.A.E.)
| | - Eva Riveira-Muñoz
- AIDS Research Institute—IrsiCaixa, 08916 Badalona, Spain; (E.B.); (R.B.); (E.R.-M.); (J.A.E.)
| | - Francesca Esposito
- Department of Life and Environmental Sciences University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (S.D.); (F.E.); (N.G.); (E.T.)
| | - Cristina Parolin
- Department of Molecular Medicine, University of Padova, 35122 Padova, Italy; (C.D.V.); (C.P.)
| | - José A. Esté
- AIDS Research Institute—IrsiCaixa, 08916 Badalona, Spain; (E.B.); (R.B.); (E.R.-M.); (J.A.E.)
- CienciaTraducida, 08391 Barcelona, Spain
| | - Nicole Grandi
- Department of Life and Environmental Sciences University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (S.D.); (F.E.); (N.G.); (E.T.)
| | - Enzo Tramontano
- Department of Life and Environmental Sciences University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Italy; (S.D.); (F.E.); (N.G.); (E.T.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), 09042 Monserrato, Cagliari, Italy
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10
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Corona A, Onnis V, Del Vecchio C, Esposito F, Cheng YC, Tramontano E. 2-(Arylamino)-6-(trifluoromethyl)nicotinic Acid Derivatives: New HIV-1 RT Dual Inhibitors Active on Viral Replication. Molecules 2020; 25:E1338. [PMID: 32183488 PMCID: PMC7144554 DOI: 10.3390/molecules25061338] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/27/2022] Open
Abstract
The persistence of the AIDS epidemic, and the life-long treatment required, indicate the constant need of novel HIV-1 inhibitors. In this scenario the HIV-1 Reverse Transcriptase (RT)-associated ribonuclease H (RNase H) function is a promising drug target. Here we report a series of compounds, developed on the 2-amino-6-(trifluoromethyl)nicotinic acid scaffold, studied as promising RNase H dual inhibitors. Among the 44 tested compounds, 34 inhibited HIV-1 RT-associated RNase H function in the low micromolar range, and seven of them showed also to inhibit viral replication in cell-based assays with a selectivity index up to 10. The most promising compound, 21, inhibited RNase H function with an IC50 of 14 µM and HIV-1 replication in cell-based assays with a selectivity index greater than 10. Mode of action studies revealed that compound 21 is an allosteric dual-site compound inhibiting both HIV-1 RT functions, blocking the polymerase function also in presence of mutations carried by circulating variants resistant to non-nucleoside inhibitors, and the RNase H function interacting with conserved regions within the RNase H domain. Proving compound 21 as a promising lead for the design of new allosteric RNase H inhibitors active against viral replication with not significant cytotoxic effects.
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Affiliation(s)
- Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Cagliari, Italy; (A.C.); (V.O.); (F.E.)
| | - Valentina Onnis
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Cagliari, Italy; (A.C.); (V.O.); (F.E.)
| | - Claudia Del Vecchio
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy;
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Cagliari, Italy; (A.C.); (V.O.); (F.E.)
| | - Yung-Chi Cheng
- Department of Pharmacology, Yale University Medical School, New Haven, CT 06520-8066, USA;
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09042 Monserrato, Cagliari, Italy; (A.C.); (V.O.); (F.E.)
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy;
- Department of Pharmacology, Yale University Medical School, New Haven, CT 06520-8066, USA;
- Genetics and Biomedical Research Institute, National Research Council, 09042 Monserrato, Italy
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11
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1,2,4-Triazolo[1,5- a]pyrimidines as a Novel Class of Inhibitors of the HIV-1 Reverse Transcriptase-Associated Ribonuclease H Activity. Molecules 2020; 25:molecules25051183. [PMID: 32151066 PMCID: PMC7179434 DOI: 10.3390/molecules25051183] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/25/2020] [Accepted: 03/03/2020] [Indexed: 12/27/2022] Open
Abstract
Despite great efforts have been made in the prevention and therapy of human immunodeficiency virus (HIV-1) infection, however the difficulty to eradicate latent viral reservoirs together with the emergence of multi-drug-resistant strains require the search for innovative agents, possibly exploiting novel mechanisms of action. In this context, the HIV-1 reverse transcriptase (RT)-associated ribonuclease H (RNase H), which is one of the few HIV-1 encoded enzymatic function still not targeted by any current drug, can be considered as an appealing target. In this work, we repurposed in-house anti-influenza derivatives based on the 1,2,4-triazolo[1,5-a]-pyrimidine (TZP) scaffold for their ability to inhibit HIV-1 RNase H function. Based on the results, a successive multi-step structural exploration around the TZP core was performed leading to identify catechol derivatives that inhibited RNase H in the low micromolar range without showing RT-associated polymerase inhibitory activity. The antiviral evaluation of the compounds in the MT4 cells showed any activity against HIV-1 (IIIB strain). Molecular modelling and mutagenesis analysis suggested key interactions with an unexplored allosteric site providing insights for the future optimization of this class of RNase H inhibitors.
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12
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Esposito F, Sechi M, Pala N, Sanna A, Koneru PC, Kvaratskhelia M, Naesens L, Corona A, Grandi N, di Santo R, D'Amore VM, Di Leva FS, Novellino E, Cosconati S, Tramontano E. Discovery of dihydroxyindole-2-carboxylic acid derivatives as dual allosteric HIV-1 Integrase and Reverse Transcriptase associated Ribonuclease H inhibitors. Antiviral Res 2019; 174:104671. [PMID: 31812637 DOI: 10.1016/j.antiviral.2019.104671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 10/25/2022]
Abstract
The management of Human Immunodeficiency Virus type 1 (HIV-1) infection requires life-long treatment that is associated with chronic toxicity and possible selection of drug-resistant strains. A new opportunity for drug intervention is offered by antivirals that act as allosteric inhibitors targeting two viral functions (dual inhibitors). In this work, we investigated the effects of 5,6-dihydroxyindole-2-carboxylic acid (DHICA) derivatives on both HIV-1 Integrase (IN) and Reverse Transcriptase associated Ribonuclease H (RNase H) activities. Among the tested compounds, the dihydroxyindole-carboxamide 5 was able to inhibit in the low micromolar range (1-18 μM) multiple functions of IN, including functional IN-IN interactions, IN-LEDGF/p75 binding and IN catalytic activity. Docking and site-directed mutagenesis studies have suggested that compound 5 binds to a previously described HIV-1 IN allosteric pocket. These observations indicate that 5 is structurally and mechanistically distinct from the published allosteric HIV-1 IN inhibitors. Moreover, compound 5 also inhibited HIV-1 RNase H function, classifying this molecule as a dual HIV-1 IN and RNase H inhibitor able to impair the HIV-1 virus replication in cell culture. Overall, we identified a new scaffold as a suitable platform for the development of novel dual HIV-1 inhibitors.
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Affiliation(s)
- Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato (CA), Italy.
| | - Mario Sechi
- Department of Chemistry and Pharmacy, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Nicolino Pala
- Department of Chemistry and Pharmacy, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Adele Sanna
- Department of Chemistry and Pharmacy, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Pratibha Chowdary Koneru
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven, B-3000, Leuven, Belgium
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato (CA), Italy
| | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato (CA), Italy
| | - Roberto di Santo
- Department of Drug Chemistry and Technologies, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Roma, Italy
| | - Vincenzo Maria D'Amore
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy
| | | | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania Luigi Vanvitelli, Via Vivaldi, 43, 81100, Caserta, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato (CA), Italy
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13
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Massari S, Corona A, Distinto S, Desantis J, Caredda A, Sabatini S, Manfroni G, Felicetti T, Cecchetti V, Pannecouque C, Maccioni E, Tramontano E, Tabarrini O. From cycloheptathiophene-3-carboxamide to oxazinone-based derivatives as allosteric HIV-1 ribonuclease H inhibitors. J Enzyme Inhib Med Chem 2019; 34:55-74. [PMID: 30362381 PMCID: PMC6211256 DOI: 10.1080/14756366.2018.1523901] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/11/2018] [Accepted: 09/11/2018] [Indexed: 11/30/2022] Open
Abstract
The paper focussed on a step-by-step structural modification of a cycloheptathiophene-3-carboxamide derivative recently identified by us as reverse transcriptase (RT)-associated ribonuclease H (RNase H) inhibitor. In particular, its conversion to a 2-aryl-cycloheptathienoozaxinone derivative and the successive thorough exploration of both 2-aromatic and cycloheptathieno moieties led to identify oxazinone-based compounds as new anti-RNase H chemotypes. The presence of the catechol moiety at the C-2 position of the scaffold emerged as critical to achieve potent anti-RNase H activity, which also encompassed anti-RNA dependent DNA polymerase (RDDP) activity for the tricyclic derivatives. Benzothienooxazinone derivative 22 resulted the most potent dual inhibitor exhibiting IC50s of 0.53 and 2.90 μM against the RNase H and RDDP functions. Mutagenesis and docking studies suggested that compound 22 binds two allosteric pockets within the RT, one located between the RNase H active site and the primer grip region and the other close to the DNA polymerase catalytic centre.
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Affiliation(s)
- Serena Massari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Jenny Desantis
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Alessia Caredda
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Tommaso Felicetti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, K.U. Leuven, Leuven, Belgium
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Monserrato, Cagliari, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
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14
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Tramontano E, Corona A, Menéndez-Arias L. Ribonuclease H, an unexploited target for antiviral intervention against HIV and hepatitis B virus. Antiviral Res 2019; 171:104613. [PMID: 31550450 DOI: 10.1016/j.antiviral.2019.104613] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/18/2022]
Abstract
Ribonucleases H (RNases H) are endonucleolytic enzymes, evolutionarily related to retroviral integrases, DNA transposases, resolvases and numerous nucleases. RNases H cleave RNA in RNA/DNA hybrids and their activity plays an important role in the replication of prokaryotic and eukaryotic genomes, as well as in the replication of reverse-transcribing viruses. During reverse transcription, the RNase H activity of human immunodeficiency virus (HIV) and hepatitis B virus (HBV) degrades the viral genomic RNA to facilitate the synthesis of viral double-stranded DNA. HIV and HBV reverse transcriptases contain DNA polymerase and RNase H domains that act in a coordinated manner to produce double-stranded viral DNA. Although RNase H inhibitors have not been developed into licensed drugs, recent progress has led to the identification of a number of small molecules with inhibitory activity at low micromolar or even nanomolar concentrations. These compounds can be classified into metal-chelating active site inhibitors and allosteric inhibitors. Among them, α-hydroxytropolones, N-hydroxyisoquinolinediones and N-hydroxypyridinediones represent chemotypes active against both HIV and HBV RNases H. In this review we summarize recent developments in the field including the identification of novel RNase H inhibitors, compounds with dual inhibitory activity, broad specificity and efforts to decrease their toxicity.
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Affiliation(s)
- Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), Madrid, Spain.
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15
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Chromenone derivatives as a versatile scaffold with dual mode of inhibition of HIV-1 reverse transcriptase-associated Ribonuclease H function and integrase activity. Eur J Med Chem 2019; 182:111617. [PMID: 31442684 DOI: 10.1016/j.ejmech.2019.111617] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/09/2019] [Accepted: 08/10/2019] [Indexed: 12/31/2022]
Abstract
A number of compounds targeting different processes of the Human Immunodeficiency Virus type 1 (HIV-1) life cycle have been developed in the continuing fight against AIDS. Coumarin-based molecules already proved to act as HIV-1 Protease (PR) or Integrase (IN) inhibitors and also to target HIV-1 reverse transcriptase (RT), blocking the DNA-dependent DNA-polymerase activity or the RNA-dependent DNA-polymerase activity working as common NNRTIs. In the present study, with the aim to exploit a coumarin-based scaffold to achieve the inhibition of multiple viral coded enzymatic functions, novel 4-hydroxy-2H, 5H-pyrano (3, 2-c) chromene-2, 5-dione derivatives were synthesized. The modeling studies calculated the theoretical binding affinity of the synthesized compounds on both HIV-1 IN and RT-associated Ribonuclease H (RNase H) active sites, which was confirmed by biological assays. Our results provide a basis for the identification of dual HIV-1 IN and RT RNase H inhibitors compounds.
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16
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Costa G, Rocca R, Corona A, Grandi N, Moraca F, Romeo I, Talarico C, Gagliardi MG, Ambrosio FA, Ortuso F, Alcaro S, Distinto S, Maccioni E, Tramontano E, Artese A. Novel natural non-nucleoside inhibitors of HIV-1 reverse transcriptase identified by shape- and structure-based virtual screening techniques. Eur J Med Chem 2018; 161:1-10. [PMID: 30342421 DOI: 10.1016/j.ejmech.2018.10.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 10/28/2022]
Abstract
In this work we report a parallel application of both docking- and shape-based virtual screening (VS) methods, followed by Molecular Dynamics simulations (MDs), for discovering new compounds able to inhibit the human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) RNA-dependent DNA polymerase activity. Specifically, we screened more than 143000 natural compounds commercially available in the ZINC database against the best five RT crystallographic models, taking into account the five approved NNRTIs as query compounds. As a result, 20 hit molecules were selected and tested on biochemical assays for the inhibition of the RNA dependent DNA polymerase RT function and, among them, an indoline pyrrolidine (hit1), an indonyl piperazine (hit2) and an indolyl indolinone (hit3) derivatives were identified as novel non-nucleoside RT inhibitors in the low micromolar range.
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Affiliation(s)
- Giosuè Costa
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Roberta Rocca
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Angela Corona
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042, Monserrato, Cagliari, Italy
| | - Nicole Grandi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042, Monserrato, Cagliari, Italy
| | - Federica Moraca
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy; Department of Chemical Sciences, University of Napoli Federico II, Via Cinthia 4, I-80126, Napoli, Italy.
| | - Isabella Romeo
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Carmine Talarico
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Maria Giovanna Gagliardi
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Francesca Alessandra Ambrosio
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
| | - Simona Distinto
- Dipartimento di Scienze della Vita e dell'Ambiente, Università degli Studi di Cagliari, Via Ospedale 72, 09124, Cagliari, Italy
| | - Elias Maccioni
- Dipartimento di Scienze della Vita e dell'Ambiente, Università degli Studi di Cagliari, Via Ospedale 72, 09124, Cagliari, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042, Monserrato, Cagliari, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro, Italy
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17
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Sanna C, Scognamiglio M, Fiorentino A, Corona A, Graziani V, Caredda A, Cortis P, Montisci M, Ceresola ER, Canducci F, Poli F, Tramontano E, Esposito F. Prenylated phloroglucinols from Hypericum scruglii, an endemic species of Sardinia (Italy), as new dual HIV-1 inhibitors effective on HIV-1 replication. PLoS One 2018; 13:e0195168. [PMID: 29601601 PMCID: PMC5877874 DOI: 10.1371/journal.pone.0195168] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/16/2018] [Indexed: 12/20/2022] Open
Abstract
In a search for new potential multitarget anti-HIV compounds from natural products, we have identified in Hypericum scruglii, an endemic and exclusive species of Sardinia (Italy), a potent plant lead. The phytochemical study of the hydroalcoholic extract obtained from its leaves led to the isolation of its most abundant secondary metabolites, belonging to different chemical classes. In particular, three phloroglucinols derivatives were identified, confirming their significance as chemotaxonomic markers of the Hypericum genus. Among them, the 3-(13-hydroxygeranyl)-1-(2'-methylbutanoyl)phloroglucinol was reported here for the first time. All six isolated compounds have been evaluated firstly for the inhibition of both Human Immunodeficiency Virus type 1 (HIV-1) Reverse Transcriptase (RT)-associated DNA Polymerase (RDDP) and Ribonuclease H (RNase H) activities, for the inhibition of HIV-1 integrase (IN) in biochemical assays, and also for their effect on viral replication. Among the isolated metabolites, three phloroglucinol derivatives and quercitrin were effective on both RT-associated RDDP and RNase H activities in biochemical assays. The same active compounds affected also HIV-1 IN strand transfer function, suggesting the involvement of the RNase H active site. Furthermore, phloroglucinols compounds, included the newly identified compound, were able to inhibit the HIV-1 replication in cell based assays.
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Affiliation(s)
- Cinzia Sanna
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
- * E-mail:
| | | | - Antonio Fiorentino
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania, Caserta, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Vittoria Graziani
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania, Caserta, Italy
| | - Alessia Caredda
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Pierluigi Cortis
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Mariofilippo Montisci
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Elisa Rita Ceresola
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Filippo Canducci
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Laboratory of Microbiology, San Raffaele Hospital, IRCCS, Milan, Italy
| | - Ferruccio Poli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
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18
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Poongavanam V, Corona A, Steinmann C, Scipione L, Grandi N, Pandolfi F, Di Santo R, Costi R, Esposito F, Tramontano E, Kongsted J. Structure-guided approach identifies a novel class of HIV-1 ribonuclease H inhibitors: binding mode insights through magnesium complexation and site-directed mutagenesis studies. MEDCHEMCOMM 2018; 9:562-575. [PMID: 30108947 PMCID: PMC6072344 DOI: 10.1039/c7md00600d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/29/2018] [Indexed: 11/21/2022]
Abstract
Persistent HIV infection requires lifelong treatment and among the 2.1 million new HIV infections that occur every year there is an increased rate of transmitted drug-resistant mutations. This fact requires a constant and timely effort in order to identify and develop new HIV inhibitors with innovative mechanisms. The HIV-1 reverse transcriptase (RT) associated ribonuclease H (RNase H) is the only viral encoded enzyme that still lacks an efficient inhibitor despite the fact that it is a well-validated target whose functional abrogation compromises viral infectivity. Identification of new drugs is a long and expensive process that can be speeded up by in silico methods. In the present study, a structure-guided screening is coupled with a similarity-based search on the Specs database to identify a new class of HIV-1 RNase H inhibitors. Out of the 45 compounds selected for experimental testing, 15 inhibited the RNase H function below 100 μM with three hits exhibiting IC50 values <10 μM. The most active compound, AA, inhibits HIV-1 RNase H with an IC50 of 5.1 μM and exhibits a Mg-independent mode of inhibition. Site-directed mutagenesis studies provide valuable insight into the binding mode of newly identified compounds; for instance, compound AA involves extensive interactions with a lipophilic pocket formed by Ala502, Lys503, and Trp (406, 426 and 535) and polar interactions with Arg557 and the highly conserved RNase H primer-grip residue Asn474. The structural insights obtained from this work provide the bases for further lead optimization.
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Affiliation(s)
- Vasanthanathan Poongavanam
- Department of Physics , Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark . ;
| | - Angela Corona
- Department of Life and Environmental Sciences , University of Cagliari , Italy .
| | - Casper Steinmann
- Department of Physics , Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark . ;
| | - Luigi Scipione
- Dipartimento di Chimica e Tecnologie del Farmaco , Istituto Pasteur-Fondazione Cenci Bolognetti , "Sapienza" Università di Roma , Roma , Italy
| | - Nicole Grandi
- Department of Life and Environmental Sciences , University of Cagliari , Italy .
| | - Fabiana Pandolfi
- Dipartimento di Chimica e Tecnologie del Farmaco , Istituto Pasteur-Fondazione Cenci Bolognetti , "Sapienza" Università di Roma , Roma , Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco , Istituto Pasteur-Fondazione Cenci Bolognetti , "Sapienza" Università di Roma , Roma , Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco , Istituto Pasteur-Fondazione Cenci Bolognetti , "Sapienza" Università di Roma , Roma , Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences , University of Cagliari , Italy .
| | - Enzo Tramontano
- Department of Life and Environmental Sciences , University of Cagliari , Italy .
- Istituto di Ricerca Genetica e Biomedica , Consiglio Nazionale delle Ricerche (CNR) , Monserrato(CA) , Italy
| | - Jacob Kongsted
- Department of Physics , Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark . ;
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19
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Corona A, di Leva FS, Rigogliuso G, Pescatori L, Madia VN, Subra F, Delelis O, Esposito F, Cadeddu M, Costi R, Cosconati S, Novellino E, di Santo R, Tramontano E. New insights into the interaction between pyrrolyl diketoacids and HIV-1 integrase active site and comparison with RNase H. Antiviral Res 2016; 134:236-243. [PMID: 27659398 DOI: 10.1016/j.antiviral.2016.09.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/16/2016] [Accepted: 09/19/2016] [Indexed: 12/18/2022]
Abstract
HIV-1 integrase (IN) inhibitors are one of the most recent innovations in the treatment of HIV infection. The selection of drug resistance viral strains is however a still open issue requiring constant efforts to identify new anti-HIV-1 drugs. Pyrrolyl diketo acid (DKA) derivatives inhibit HIV-1 replication by interacting with the Mg2+ cofactors within the HIV-1 IN active site or within the HIV-1 reverse-transcriptase associated ribonuclease H (RNase H) active site. While the interaction mode of pyrrolyl DKAs with the RNase H active site has been recently reported and substantiated by mutagenesis experiments, their interaction within the IN active site still lacks a detailed understanding. In this study, we investigated the binding mode of four pyrrolyl DKAs to the HIV-1 IN active site by molecular modeling coupled with site-directed mutagenesis studies showing that the DKA pyrrolyl scaffold primarily interacts with the IN amino residues P145, Q146 and Q148. Importantly, the tested DKAs demonstrated good effectiveness against HIV-1 Raltegravir resistant Y143A and N155H INs, thus showing an interaction pattern with relevant differences if compared with the first generation IN inhibitors. These data provide precious insights for the design of new HIV inhibitors active on clinically selected Raltegravir resistant variants. Furthermore, this study provides new structural information to modulate IN and RNase H inhibitory activities for development of dual-acting anti-HIV agents.
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Affiliation(s)
- Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy
| | - Francesco Saverio di Leva
- Department of Pharmacy, University of Naples "Federico II", Via Domenico Montesano, 49 80131, Naples, Italy
| | - Giuseppe Rigogliuso
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy; LBPA, ENS Cachan, CNRS, 61 Avenue du président Wilson, 94235, Cachan Cedex, France
| | - Luca Pescatori
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Valentina Noemi Madia
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Frederic Subra
- LBPA, ENS Cachan, CNRS, 61 Avenue du président Wilson, 94235, Cachan Cedex, France
| | - Olivier Delelis
- LBPA, ENS Cachan, CNRS, 61 Avenue du président Wilson, 94235, Cachan Cedex, France
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy
| | - Marta Cadeddu
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Sandro Cosconati
- DiSTABiF, Seconda Università di Napoli, Via Vivaldi, 43, 81100, Caserta, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", Via Domenico Montesano, 49 80131, Naples, Italy
| | - Roberto di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy.
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20
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Development of Potent Antiviral Drugs Inspired by Viral Hexameric DNA-Packaging Motors with Revolving Mechanism. J Virol 2016; 90:8036-46. [PMID: 27356896 DOI: 10.1128/jvi.00508-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intracellular parasitic nature of viruses and the emergence of antiviral drug resistance necessitate the development of new potent antiviral drugs. Recently, a method for developing potent inhibitory drugs by targeting biological machines with high stoichiometry and a sequential-action mechanism was described. Inspired by this finding, we reviewed the development of antiviral drugs targeting viral DNA-packaging motors. Inhibiting multisubunit targets with sequential actions resembles breaking one bulb in a series of Christmas lights, which turns off the entire string. Indeed, studies on viral DNA packaging might lead to the development of new antiviral drugs. Recent elucidation of the mechanism of the viral double-stranded DNA (dsDNA)-packaging motor with sequential one-way revolving motion will promote the development of potent antiviral drugs with high specificity and efficiency. Traditionally, biomotors have been classified into two categories: linear and rotation motors. Recently discovered was a third type of biomotor, including the viral DNA-packaging motor, beside the bacterial DNA translocases, that uses a revolving mechanism without rotation. By analogy, rotation resembles the Earth's rotation on its own axis, while revolving resembles the Earth's revolving around the Sun (see animations at http://rnanano.osu.edu/movie.html). Herein, we review the structures of viral dsDNA-packaging motors, the stoichiometries of motor components, and the motion mechanisms of the motors. All viral dsDNA-packaging motors, including those of dsDNA/dsRNA bacteriophages, adenoviruses, poxviruses, herpesviruses, mimiviruses, megaviruses, pandoraviruses, and pithoviruses, contain a high-stoichiometry machine composed of multiple components that work cooperatively and sequentially. Thus, it is an ideal target for potent drug development based on the power function of the stoichiometries of target complexes that work sequentially.
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