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Giannakopoulou E, Pardali V, Edwards TC, Woodson M, Tajwar R, Tavis JE, Zoidis G. Identification and assessment of the 1,6-dihydroxy-pyridin-2-one moiety as privileged scaffold for HBV ribonuclease H inhibition. Antiviral Res 2024; 223:105833. [PMID: 38325606 DOI: 10.1016/j.antiviral.2024.105833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/20/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
The Hepatitis B Virus (HBV) ribonuclease H (RNase H) although promising remains an unexploited therapeutic target. HBV RNase H inhibition causes premature termination of viral minus-polarity DNA strands, prevents the synthesis of the viral positive-polarity DNA strand, and causes accumulation of RNA:DNA heteroduplexes within viral capsids. As part of our ongoing research to develop more potent anti-HBV RNase H inhibitors, we designed, synthesized and analyzed a library of 18 novel compounds (17 N-hydroyxpyridinedione (HPD) imine derivatives and 1 barbituric acid analogue) as potential leads for HBV treatment development. In cell assays, fourteen HPDs showed significant anti-HBV activity with EC50s from 1.1 to 2.5 μM and selectivity indices (SI) of up to 58. Three of them exhibited more than 3-fold improvement in the SI over the best previous HPD imine (SI = 13). To gain insight to the interaction between the tested compounds and the active site of HBV RNase H, docking experiments were undertaken. In almost all binding poses, the novel HPDs coordinated both active site Mg2+ ions via their oxygen trident. Furthermore, the novel HPDs displayed high cell permeability and solubility as well as good drug-like properties. These results reveal that HPD imines can be significantly active and selective HBV inhibitors, and that the HPD scaffold merits further development towards anti-HBV agents.
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Affiliation(s)
- Erofili Giannakopoulou
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771, Athens, Greece
| | - Vasiliki Pardali
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771, Athens, Greece
| | - Tiffany C Edwards
- Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, 63104, United States
| | - Molly Woodson
- Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, 63104, United States
| | - Razia Tajwar
- Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, 63104, United States
| | - John E Tavis
- Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, 63104, United States
| | - Grigoris Zoidis
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771, Athens, Greece.
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2
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Mandova T, Saivish MV, Menezes GDL, Bezerra KS, Fulco UL, da Silva RA, Da Costa FB, Nogueira ML. Antiviral Activity and Molecular Dynamics Simulation of Hops Compounds against Oropouche Virus ( Peribunyaviridae). Pharmaceutics 2023; 15:2769. [PMID: 38140109 PMCID: PMC10747393 DOI: 10.3390/pharmaceutics15122769] [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: 09/20/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
The Oropouche virus (OROV) is a member of the family Peribunyaviridae (order Bunyavirales) and the cause of a dengue-like febrile illness transmitted mainly by biting midges and mosquitoes. In this study, we aimed to explore acylphloroglucinols and xanthohumol from hops (Humulus lupulus L.) as a promising alternative for antiviral therapies. The evaluation of the inhibitory potential of hops compounds on the viral cycle of OROV was performed through two complementary approaches. The first approach applies cell-based assay post-inoculation experiments to explore the inhibitory potential on the latest steps of the viral cycle, such as genome translation, replication, virion assembly, and virion release from the cells. The second part covers in silico methods evaluating the ability of those compounds to inhibit the activity of the endonuclease domain, which is essential for transcription, binding, and cleaving RNA. In conclusion, the beta acids showed strongest inhibitory potential in post-treatment assay (EC50 = 26.7 µg/mL). Xanthohumol had the highest affinity for OROV endonuclease followed by colupulone and cohumulone. This result contrasts with that observed for docking and MM/PBSA analysis, where cohumulone was found to have a higher affinity. Finally, among the three tested ligands, Lys92 and Arg33 exhibited the highest affinity with the protein.
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Affiliation(s)
- Tsvetelina Mandova
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-020, SP, Brazil
- Gilson Purification, 22 rue Bourseul, 56890 Saint Avé, France
| | - Marielena Vogel Saivish
- Laboratórios de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil; (M.V.S.)
- Brazilian Biosciences National Laboratory, Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-100, SP, Brazil
| | - Gabriela de Lima Menezes
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil; (G.d.L.M.); (U.L.F.)
| | - Katyanna Sales Bezerra
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil; (G.d.L.M.); (U.L.F.)
| | - Umberto Laino Fulco
- Bioinformatics Multidisciplinary Environment, Programa de Pós Graduação em Bioinformática, Universidade Federal do Rio Grande do Norte, Natal 59078-400, RN, Brazil; (G.d.L.M.); (U.L.F.)
| | | | - Fernando Batista Da Costa
- AsterBioChem Research Team, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-020, SP, Brazil
| | - Maurício Lacerda Nogueira
- Laboratórios de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto, São José do Rio Preto 15090-000, SP, Brazil; (M.V.S.)
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
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3
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Ito Y, Lu H, Kitajima M, Ishikawa H, Nakata Y, Iwatani Y, Hoshino T. Sticklac-Derived Natural Compounds Inhibiting RNase H Activity of HIV-1 Reverse Transcriptase. JOURNAL OF NATURAL PRODUCTS 2023; 86:2487-2495. [PMID: 37874155 DOI: 10.1021/acs.jnatprod.3c00662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The emergence of drug-resistant viruses is a serious concern in current chemotherapy for human immunodeficiency virus type-1 (HIV-1) infectious diseases. Hence, antiviral drugs aiming at targets that are different from those of approved drugs are still required, and the RNase H activity of HIV-1 reverse transcriptase is a suitable target. In this study, a search of a series of natural compounds was performed to identify the RNase H inhibitors. Three compounds were found to block the RNase H enzymatic activity. A laccaic acid skeleton was observed in all three natural compounds. A hydroxy phenyl group is connected to an anthraquinone backbone in the skeleton. An acetamido-ethyl, amino-carboxy-ethyl, and amino-ethyl are bound to the phenyl in laccaic acids A, C, and E, respectively. Laccaic acid C showed a 50% inhibitory concentration at 8.1 μM. Laccaic acid C also showed inhibitory activity in a cell-based viral proliferation assay. Binding structures of these three laccaic acids were determined by X-ray crystallographic analysis using a recombinant protein composed of the HIV-1 RNase H domain. Two divalent metal ions were located at the catalytic center in which one carbonyl and two hydroxy groups on the anthraquinone backbone chelated two metal ions. Molecular dynamics simulations were performed to examine the stabilities of the binding structures. Laccaic acid C showed the strongest binding to the catalytic site. These findings will be helpful for the design of potent inhibitors with modification of laccaic acids to enhance the binding affinity.
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Affiliation(s)
- Yuma Ito
- Laboratory of Molecular Design, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Huiyan Lu
- Laboratory of Molecular Design, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Mariko Kitajima
- Laboratory of Middle Molecular Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Hayato Ishikawa
- Laboratory of Middle Molecular Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Yoshihiro Nakata
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi 460-0001, Japan
| | - Yasumasa Iwatani
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center, 4-1-1 Sannomaru, Naka-ku, Nagoya, Aichi 460-0001, Japan
- Department of AIDS Research, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Tyuji Hoshino
- Laboratory of Molecular Design, Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
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4
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Ghafoor NA, Kırboğa KK, Baysal Ö, Süzek BE, Silme RS. Data mining and molecular dynamics analysis to detect HIV-1 reverse transcriptase RNase H activity inhibitor. Mol Divers 2023:10.1007/s11030-023-10707-6. [PMID: 37561229 DOI: 10.1007/s11030-023-10707-6] [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: 05/30/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023]
Abstract
HIV-1 is a deadly virus that affects millions of people worldwide. In this study, we aimed to inhibit viral replication by targeting one of the HIV-1 proteins and identifying a new drug candidate. We used data mining and molecular dynamics methods on HIV-1 genomes. Based on MAUVE analysis, we selected the RNase H activity of the reverse transcriptase (R.T) enzyme as a potential target due to its low mutation rate and high conservation level. We screened about 94,000 small molecule inhibitors by virtual screening. We validated the hit compounds' stability and binding free energy through molecular dynamics simulations and MM/PBSA. Phomoarcherin B, known for its anticancer properties, emerged as the best candidate and showed potential as an HIV-1 reverse transcriptase RNase H activity inhibitor. This study presents a new target and drug candidate for HIV-1 treatment. However, in vitro and in vivo tests are required. Also, the effect of RNase H activity on viral replication and the interaction of Phomoarcherin B with other HIV-1 proteins should be investigated.
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Affiliation(s)
- Naeem Abdul Ghafoor
- Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, Kötekli, 48121, Muğla, Turkey
| | - Kevser Kübra Kırboğa
- Bioengineering Department, Bilecik Seyh Edebali University, 11230, Bilecik, Turkey
- Informatics Institute, Istanbul Technical University, Maslak, 34469, Istanbul, Turkey
| | - Ömür Baysal
- Molecular Microbiology Unit, Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, Kötekli, 48121, Muğla, Turkey.
| | - Barış Ethem Süzek
- Department of Computer Engineering, Faculty of Engineering, Muğla Sıtkı Koçman University, Kötekli, 48000, Muğla, Turkey
| | - Ragıp Soner Silme
- Center for Research and Practice in Biotechnology and Genetic Engineering, Istanbul University, Vezneciler, Fatih, 34119, Istanbul, Turkey
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Rezaei M, Fooladi P, Norani M, Crawford A, Eisa-Beygi S, Tahamtani Y, Ayyari M. Investigation of Kelussia Odoratissima and Angelica Sinensis Similarities in Zebrafish-based In-vivo Bioactivity Assays and Their Chemical Composition. Galen Med J 2023; 12:1-12. [PMID: 38774850 PMCID: PMC11108663 DOI: 10.31661/gmj.v12i.2793] [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: 11/07/2022] [Indexed: 05/24/2024] Open
Abstract
BACKGROUND Kelussia odoratissima and Angelica sinensis are two medicinal plants commonly used in Iran and China, respectively. They have been used in their indigenous traditional medicine, for various diseases including, blood refining, inflammation, cold, flu, stress, cardiovascular diseases, and nervous disorders. This study was conducted to evaluate the volatile oil composition of K. odoratissima leaves (KVL) and A. sinensis root (AVR); we also examined the biological activity of essential oils (EOs) and hydroalcoholic extracts of both plants using two different transgenic zebrafish (Danio rerio) models: angiogenesis and pancreatic beta cell (pBC) regeneration models. MATERIALS AND METHODS Both EOs were isolated by hydrodistillation and analysed by GC and GC/MS. For viability tests, larvae were treated with different concentrations of extracts to determine an appropriate starting concentration. Hydroalcoholic extracts and EOs have been tested in a dose-dependent manner for their biological activity using tissue-specific transgenic zebrafish Tg(fli-1: EGFP) and Tg (ins: GFP-NTR) embryos and larvae. One-way ANOVA was used to compare the mean of pBC area and intersegmental vessels (ISVs) outgrowth between the treatment groups. RESULTS Eleven compounds were in common to both oils, comprising 51.3% of KVL and 61.7% of AVR, of which 39.3% in KVL and 37.6% in AVR were phthalide structures. Results revealed that both EOs blocked ISVs formation in the Tg (fli-1: EGFP) embryos increased to 10% of the control value, while both hydroalcoholic extracts did not show any anti-angiogenesis effects in these embryos. In addition, AVR has been shown to significantly induce PBC regeneration following ablation in the Tg (ins: GFP-NTR), but its regenerative activity was lower than that of 5'-N-ethylcarboxamidoadenosine (NECA) as a positive control. Taken together, the anti-angiogenesis activity of both EOs could be attributed to the phthalide structures while for the PBC regenerative activity, other compounds including β-Thujaplicinol, exclusively existing in AVR, might be effective. CONCLUSION Although the genera, organs, and origin of these plants are different, their similar chemical composition and biological activities make them valuable resources for further investigation in basic medical and pharmaceutical science.
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Affiliation(s)
- Mohammad Rezaei
- Department of Stem Cells and Developmental Biology, Cell Science Research Centre,
Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Parisa Fooladi
- Department of Stem Cells and Developmental Biology, Cell Science Research Centre,
Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Mohamad Norani
- Department of Horticultural Science, Tarbiat Modares University, Tehran, Iran
| | - Alexander Crawford
- Department of Horticultural Science, Tarbiat Modares University, Tehran, Iran
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Shahram Eisa-Beygi
- Department of Radiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Yaser Tahamtani
- Department of Stem Cells and Developmental Biology, Cell Science Research Centre,
Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Reproductive Epidemiology Research Center, Royan Institute for Reproductive
Biomedicine, ACECR, Tehran, Iran
| | - Mahdi Ayyari
- Department of Horticultural Science, Tarbiat Modares University, Tehran, Iran
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Corona A, Meleddu R, Delelis O, Subra F, Cottiglia F, Esposito F, Distinto S, Maccioni E, Tramontano E. 5-Nitro-3-(2-(4-phenylthiazol-2-yl)hydrazineylidene)indolin-2-one derivatives inhibit HIV-1 replication by a multitarget mechanism of action. Front Cell Infect Microbiol 2023; 13:1193280. [PMID: 37424782 PMCID: PMC10328743 DOI: 10.3389/fcimb.2023.1193280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/25/2023] [Indexed: 07/11/2023] Open
Abstract
In the effort to identify and develop new HIV-1 inhibitors endowed with innovative mechanisms, we focused our attention on the possibility to target more than one viral encoded enzymatic function with a single molecule. In this respect, we have previously identified by virtual screening a new indolinone-based scaffold for dual allosteric inhibitors targeting both reverse transcriptase-associated functions: polymerase and RNase H. Pursuing with the structural optimization of these dual inhibitors, we synthesized a series of 35 new 3-[2-(4-aryl-1,3-thiazol-2-ylidene)hydrazin-1-ylidene]1-indol-2-one and 3-[3-methyl-4-arylthiazol-2-ylidene)hydrazine-1-ylidene)indolin-2-one derivatives, which maintain their dual inhibitory activity in the low micromolar range. Interestingly, compounds 1a, 3a, 10a, and 9b are able to block HIV-1 replication with EC50 < 20 µM. Mechanism of action studies showed that such compounds could block HIV-1 integrase. In particular, compound 10a is the most promising for further multitarget compound development.
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Affiliation(s)
- Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Rita Meleddu
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Olivier Delelis
- Laboratory of Biology and Applied Pharmacology (LBPA), Ecole Normale Supérieure (ENS) Cachan, Centre National de la Recherche Scientifique (CNRS), Cachan, France
| | - Frederic Subra
- Laboratory of Biology and Applied Pharmacology (LBPA), Ecole Normale Supérieure (ENS) Cachan, Centre National de la Recherche Scientifique (CNRS), Cachan, France
| | - Filippo Cottiglia
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Simona Distinto
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Elias Maccioni
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Monserrato, Italy
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7
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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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Ranga A, Gupta A, Yadav L, Kumar S, Jain P. Advancing beyond reverse transcriptase inhibitors: The new era of hepatitis B polymerase inhibitors. Eur J Med Chem 2023; 257:115455. [PMID: 37216809 DOI: 10.1016/j.ejmech.2023.115455] [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: 02/28/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023]
Abstract
Hepatitis B virus (HBV) is a genetically diverse blood-borne virus responsible for chronic hepatitis B. The HBV polymerase plays a key role in viral genome replication within the human body and has been identified as a potential drug target for chronic hepatitis B therapeutics. However, available nucleotide reverse transcriptase inhibitors only target the reverse transcriptase domain of the HBV polymerase; they also pose resistance issues and require lifelong treatment that can burden patients financially. In this study, various chemical classes are reviewed that have been developed to target different domains of the HBV polymerase: Terminal protein, which plays a vital role in the formation of the viral DNA; Reverse transcriptase, which is responsible for the synthesis of the viral DNA from RNA, and; Ribonuclease H, which is responsible for degrading the RNA strand in the RNA-DNA duplex formed during the reverse transcription process. Host factors that interact with the HBV polymerase to achieve HBV replication are also reviewed; these host factors can be targeted by inhibitors to indirectly inhibit polymerase functionality. A detailed analysis of the scope and limitations of these inhibitors from a medicinal chemistry perspective is provided. The structure-activity relationship of these inhibitors and the factors that may affect their potency and selectivity are also examined. This analysis will be useful in supporting the further development of these inhibitors and in designing new inhibitors that can inhibit HBV replication more efficiently.
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Affiliation(s)
- Abhishek Ranga
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Aarti Gupta
- Department of Pharmaceutical Biotechnology, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Laxmi Yadav
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Sachin Kumar
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India.
| | - Priti Jain
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India.
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9
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Lu H, Komukai Y, Usami K, Guo Y, Qiao X, Nukaga M, Hoshino T. Computational and Crystallographic Analysis of Binding Structures of Inhibitory Compounds for HIV-1 RNase H Activity. J Chem Inf Model 2022; 62:6762-6774. [PMID: 36184946 DOI: 10.1021/acs.jcim.2c00537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chemotherapy of human immunodeficiency virus type-1 (HIV-1) has significantly developed over the last three decades. The emergence of drug-resistant variants is, however, still a severe problem. The RNase H activity of HIV-1 reverse transcriptase is an attractive target for a new class of antiviral drugs because there is no approved inhibitor. The nitro-furan-carbonyl and nitro-thiophene-carbonyl groups are potent scaffolds for the HIV-1 RNase H inhibitor. In this work, the binding structures of six inhibitory compounds were obtained by X-ray crystal analysis in a complex with a recombinant protein of HIV-1 RNase H domain. Every inhibitory compound was found to be bound to the catalytic site with the furan- or thiophene-ring coordinated to two divalent metal ions at the binding pocket. All the atoms in nitro, furan, carbonyl, and two metals were aligned in the nitro-furan derivatives. The straight line connecting nitro and carboxyl groups was parallel to the plane made by two metal ions and a furan O atom. The binding modes of the nitro-thiophene derivatives were slightly different from those of the nitro-furan ones. The nitro and carbonyl groups deviated from the plane made by two metals and a thiophene S atom. Molecular dynamics simulations suggested that the furan O or thiophene S atom and carbonyl O atom were firmly coordinated to the metal ions. The simulations made the planar nitro-furan moiety well aligned to the line connecting the two metal ions. In contrast, the nitro-thiophene derivatives were displaced from the initial positions after the simulations. The computational findings will be a sound basis for developing potent inhibitors for HIV-1 RNase H activity.
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Affiliation(s)
- Huiyan Lu
- Graduate School of Pharmaceutical Sciences, Chiba University Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Yuji Komukai
- Graduate School of Pharmaceutical Sciences, Chiba University Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Koto Usami
- Graduate School of Pharmaceutical Sciences, Chiba University Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Yan Guo
- Graduate School of Pharmaceutical Sciences, Chiba University Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Xinyue Qiao
- Graduate School of Pharmaceutical Sciences, Chiba University Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
| | - Michiyoshi Nukaga
- Faculty of Pharmaceutical Sciences, Josai International University Gumyo 1, Togane-shi Chiba 283-8555, Japan
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University Inohana 1-8-1, Chuo-ku, Chiba 260-8675, Japan
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10
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Tajwar R, Bradley DP, Ponzar NL, Tavis JE. Predicted structure of the hepatitis B virus polymerase reveals an ancient conserved protein fold. Protein Sci 2022; 31:e4421. [PMID: 36173165 PMCID: PMC9601786 DOI: 10.1002/pro.4421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 11/12/2022]
Abstract
Hepatitis B virus (HBV) chronically infects >250 million people. It replicates by a unique protein-primed reverse transcription mechanism, and the primary anti-HBV drugs are nucleos(t)ide analogs targeting the viral polymerase (P). P has four domains compared to only two in most reverse transcriptases: the terminal protein (TP) that primes DNA synthesis, a spacer, the reverse transcriptase (RT), and the ribonuclease H (RNase H). Despite being a major drug target and catalyzing a reverse transcription pathway very different from the retroviruses, HBV P has resisted structural analysis for decades. Here, we exploited computational advances to model P. The TP wrapped around the RT domain rather than forming the anticipated globular domain, with the priming tyrosine poised over the RT active site. The orientation of the RT and RNase H domains resembled that of the retroviral enzymes despite the lack of sequences analogous to the retroviral linker region. The model was validated by mapping residues with known surface exposures, docking nucleic acids, mechanistically interpreting mutations with strong phenotypes, and docking inhibitors into the RT and RNase H active sites. The HBV P fold, including the orientation of the TP domain, was conserved among hepadnaviruses infecting rodent to fish hosts and a nackednavirus, but not in other non-retroviral RTs. Therefore, this protein fold has persisted since the hepadnaviruses diverged from nackednaviruses >400 million years ago. This model will advance mechanistic analyses into the poorly understood enzymology of HBV reverse transcription and will enable drug development against non-active site targets for the first time.
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Affiliation(s)
- Razia Tajwar
- Department of Molecular Microbiology and Immunology, School of Medicine and Institute for Drug and Biotherapeutic InnovationSaint Louis UniversitySaint LouisMissouriUSA
| | - Daniel P. Bradley
- Department of Molecular Microbiology and Immunology, School of Medicine and Institute for Drug and Biotherapeutic InnovationSaint Louis UniversitySaint LouisMissouriUSA
| | - Nathan L. Ponzar
- Department of Molecular Microbiology and Immunology, School of Medicine and Institute for Drug and Biotherapeutic InnovationSaint Louis UniversitySaint LouisMissouriUSA
| | - John E. Tavis
- Department of Molecular Microbiology and Immunology, School of Medicine and Institute for Drug and Biotherapeutic InnovationSaint Louis UniversitySaint LouisMissouriUSA
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11
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Geerling E, Murphy V, Mai MC, Stone ET, Casals AG, Hassert M, O’Dea AT, Cao F, Donlin MJ, Elagawany M, Elgendy B, Pardali V, Giannakopoulou E, Zoidis G, Schiavone DV, Berkowitz AJ, Agyemang NB, Murelli RP, Tavis JE, Pinto AK, Brien JD. Metal coordinating inhibitors of Rift Valley fever virus replication. PLoS One 2022; 17:e0274266. [PMID: 36112605 PMCID: PMC9481026 DOI: 10.1371/journal.pone.0274266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
Rift Valley fever virus (RVFV) is a veterinary and human pathogen and is an agent of bioterrorism concern. Currently, RVFV treatment is limited to supportive care, so new drugs to control RVFV infection are urgently needed. RVFV is a member of the order Bunyavirales, whose replication depends on the enzymatic activity of the viral L protein. Screening for RVFV inhibitors among compounds with divalent cation-coordinating motifs similar to known viral nuclease inhibitors identified 47 novel RVFV inhibitors with selective indexes from 1.1–103 and 50% effective concentrations of 1.2–56 μM in Vero cells, primarily α-Hydroxytropolones and N-Hydroxypyridinediones. Inhibitor activity and selective index was validated in the human cell line A549. To evaluate specificity, select compounds were tested against a second Bunyavirus, La Crosse Virus (LACV), and the flavivirus Zika (ZIKV). These data indicate that the α-Hydroxytropolone and N-Hydroxypyridinedione chemotypes should be investigated in the future to determine their mechanism(s) of action allowing further development as therapeutics for RVFV and LACV, and these chemotypes should be evaluated for activity against related pathogens, including Hantaan virus, severe fever with thrombocytopenia syndrome virus, Crimean-Congo hemorrhagic fever virus.
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Affiliation(s)
- Elizabeth Geerling
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Valerie Murphy
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Maria C. Mai
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - E. Taylor Stone
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Andreu Gazquez Casals
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Mariah Hassert
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Austin T. O’Dea
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Feng Cao
- John Cochran Division, Department of Veterans Affairs Medical Center, Saint Louis, Missouri, United States of America
| | - Maureen J. Donlin
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Mohamed Elagawany
- Center for Clinical Pharmacology, Washington University School of Medicine and University of Health Sciences and Pharmacy, Saint Louis, Missouri, United States of America
| | - Bahaa Elgendy
- Center for Clinical Pharmacology, Washington University School of Medicine and University of Health Sciences and Pharmacy, Saint Louis, Missouri, United States of America
- Department of Pharmaceutical and Administrative Sciences, University of Health Sciences and Pharmacy, Saint Louis, Missouri, United States of America
| | - Vasiliki Pardali
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Erofili Giannakopoulou
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Grigoris Zoidis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Daniel V. Schiavone
- Department of Chemistry and The Graduate Center of The City University of New York, Brooklyn College, The City University of New York, Brooklyn, New York, United States of America
| | - Alex J. Berkowitz
- Department of Chemistry and The Graduate Center of The City University of New York, Brooklyn College, The City University of New York, Brooklyn, New York, United States of America
| | - Nana B. Agyemang
- Department of Chemistry and The Graduate Center of The City University of New York, Brooklyn College, The City University of New York, Brooklyn, New York, United States of America
| | - Ryan P. Murelli
- Department of Chemistry and The Graduate Center of The City University of New York, Brooklyn College, The City University of New York, Brooklyn, New York, United States of America
| | - John E. Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Amelia K. Pinto
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - James D. Brien
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
- * E-mail:
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12
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Insights into HIV-1 Reverse Transcriptase (RT) Inhibition and Drug Resistance from Thirty Years of Structural Studies. Viruses 2022; 14:v14051027. [PMID: 35632767 PMCID: PMC9148108 DOI: 10.3390/v14051027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
The enzyme reverse transcriptase (RT) plays a central role in the life cycle of human immunodeficiency virus (HIV), and RT has been an important drug target. Elucidations of the RT structures trapping and detailing the enzyme at various functional and conformational states by X-ray crystallography have been instrumental for understanding RT activities, inhibition, and drug resistance. The structures have contributed to anti-HIV drug development. Currently, two classes of RT inhibitors are in clinical use. These are nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). However, the error-prone viral replication generates variants that frequently develop resistance to the available drugs, thus warranting a continued effort to seek more effective treatment options. RT also provides multiple additional potential druggable sites. Recently, the use of single-particle cryogenic electron microscopy (cryo-EM) enabled obtaining structures of NNRTI-inhibited HIV-1 RT/dsRNA initiation and RT/dsDNA elongation complexes that were unsuccessful by X-ray crystallography. The cryo-EM platform for the structural study of RT has been established to aid drug design. In this article, we review the roles of structural biology in understanding and targeting HIV RT in the past three decades and the recent structural insights of RT, using cryo-EM.
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13
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Alpha-hydroxytropolones are noncompetitive inhibitors of human RNase H1 that bind to the active site and modulate substrate binding. J Biol Chem 2022; 298:101790. [PMID: 35247386 PMCID: PMC9034292 DOI: 10.1016/j.jbc.2022.101790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 11/23/2022] Open
Abstract
The ribonucleases H (RNases H) of HIV and hepatitis B virus are type 1 RNases H that are promising drug targets because inhibiting their activity blocks viral replication. Eukaryotic ribonuclease H1 (RNase H1) is an essential protein and a probable off-target enzyme for viral RNase H inhibitors. α-hydroxytropolones (αHTs) are a class of anti-RNase H inhibitors that can inhibit the HIV, hepatitis B virus, and human RNases H1; however, it is unclear how these inhibitors could be developed to distinguish between these enzymes. To accelerate the development of selective RNase H inhibitors, we performed biochemical and kinetic studies on the human enzyme, which was recombinantly expressed in Escherichia coli. Size-exclusion chromatography showed that free RNase H1 is monomeric and forms a 2:1 complex with a substrate of 12 bp. FRET heteroduplex cleavage assays were used to test inhibition of RNase H1 in steady-state kinetics by two structurally diverse αHTs, 110 and 404. We determined that turnover rate was reduced, but inhibition was not competitive with substrate, despite inhibitor binding to the active site. Given the compounds’ reversible binding to the active site, we concluded that traditional noncompetitive and mixed inhibition mechanisms are unlikely. Instead, we propose a model in which, by binding to the active site, αHTs stabilize an inactive enzyme–substrate–inhibitor complex. This new model clarifies the mechanism of action of αHTs against RNase H1 and will aid the development of RNase H inhibitors selective for the viral enzymes.
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14
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Ilina TV, Brosenitsch T, Sluis-Cremer N, Ishima R. Retroviral RNase H: Structure, mechanism, and inhibition. Enzymes 2021; 50:227-247. [PMID: 34861939 DOI: 10.1016/bs.enz.2021.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
All retroviruses encode the enzyme, reverse transcriptase (RT), which is involved in the conversion of the single-stranded viral RNA genome into double-stranded DNA. RT is a multifunctional enzyme and exhibits DNA polymerase and ribonuclease H (RNH) activities, both of which are essential to the reverse-transcription process. Despite the successful development of polymerase-targeting antiviral drugs over the last three decades, no bona fide inhibitor against the RNH activity of HIV-1 RT has progressed to clinical evaluation. In this review article, we describe the retroviral RNH function and inhibition, with primary consideration of the structural aspects of inhibition.
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Affiliation(s)
- Tatiana V Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Teresa Brosenitsch
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Nicolas Sluis-Cremer
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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15
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Abstract
Hepatitis B virus (HBV) is a hepatotropic, partially double-stranded DNA virus that replicates by reverse transcription and is a major cause of chronic liver disease and hepatocellular carcinoma. Reverse transcription is catalyzed by the four-domain multifunctional HBV polymerase (P) protein that has protein-priming, RNA- and DNA-dependent DNA synthesis (i.e., reverse transcriptase), and ribonuclease H activities. P also likely promotes the three strand transfers that occur during reverse transcription, and it may participate in immune evasion by HBV. Reverse transcription is primed by a tyrosine residue in the amino-terminal domain of P, and P remains covalently attached to the product DNA throughout reverse transcription. The reverse transcriptase activity of P is the target for the nucleos(t)ide analog drugs that dominate HBV treatment, and P is the target of ongoing efforts to develop new drugs against both the reverse transcriptase and ribonuclease H activities. Despite the unusual reverse transcription pathway catalyzed by P and the importance of P to HBV therapy, understanding the enzymology and structure of HBV P severely lags that of the retroviral reverse transcriptases due to substantial technical challenges to studying the enzyme. Obtaining a better understanding of P will broaden our appreciation of the diversity among reverse transcribing elements in nature, and will help improve treatment for people chronically infected with HBV.
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Affiliation(s)
- Daniel N Clark
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Razia Tajwar
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, United States
| | - Jianming Hu
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, United States.
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16
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Pyrroles as Privileged Scaffolds in the Search for New Potential HIV Inhibitors. Pharmaceuticals (Basel) 2021; 14:ph14090893. [PMID: 34577593 PMCID: PMC8468532 DOI: 10.3390/ph14090893] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/04/2023] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) is caused by human immunodeficiency virus (HIV) and remains a global health problem four decades after the report of its first case. Despite success in viral load suppression and the increase in patient survival due to combined antiretroviral therapy (cART), the development of new drugs has become imperative due to strains that have become resistant to antiretrovirals. In this context, there has been a continuous search for new anti-HIV agents based on several chemical scaffolds, including nitrogenated heterocyclic pyrrole rings, which have been included in several compounds with antiretroviral activity. Thus, this review aims to describe pyrrole-based compounds with anti-HIV activity as a new potential treatment against AIDS, covering the period between 2015 and 2020. Our research allowed us to conclude that pyrrole derivatives are still worth exploring, as they may provide highly active compounds targeting different steps of the HIV-1 replication cycle and act with an innovative mechanism.
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17
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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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18
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Saeed AFUH, Chan C, Guan H, Gong B, Guo P, Cheng X, Ouyang S. Structural Insights into gp16 ATPase in the Bacteriophage ϕ29 DNA Packaging Motor. Biochemistry 2021; 60:886-897. [PMID: 33689296 DOI: 10.1021/acs.biochem.0c00935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Biological motors, ubiquitous in living systems, convert chemical energy into different kinds of mechanical motions critical to cellular functions. Gene product 16 (gp16) in bacteriophage ϕ29 is among the most powerful biomotors known, which adopts a multisubunit ring-shaped structure and hydrolyzes ATP to package double-stranded DNA (dsDNA) into a preformed procapsid. Here we report the crystal structure of the C-terminal domain of gp16 (gp16-CTD). Structure-based alignment and molecular dynamics simulations revealed an essential binding surface of gp16-CTD for prohead RNA, a unique component of the motor complex. Furthermore, our simulations highlighted a dynamic interplay between the N-terminal domain and the CTD of gp16, which may play a role in driving movement of DNA into the procapsid. Lastly, we assembled an atomic structural model of the complete ϕ29 dsDNA packaging motor complex by integrating structural and experimental data from multiple sources. Collectively, our findings provided a refined inchworm-revolution model for dsDNA translocation in bacteriophage ϕ29 and suggested how the individual domains of gp16 work together to power such translocation.
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Affiliation(s)
- Abdullah F U H Saeed
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China.,College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350117, China
| | - Chun Chan
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Hongxin Guan
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Bing Gong
- Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Beibu Gulf University, Qinzhou 535000, China
| | - Peixuan Guo
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States.,Center for RNA Nanobiotechnology and Nanomedicine, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xiaolin Cheng
- College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States.,Biophysics Graduate Program and Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio 43210, United States
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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19
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Todd B, Tchesnokov EP, Götte M. The active form of the influenza cap-snatching endonuclease inhibitor baloxavir marboxil is a tight binding inhibitor. J Biol Chem 2021; 296:100486. [PMID: 33647314 PMCID: PMC8065212 DOI: 10.1016/j.jbc.2021.100486] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 12/11/2022] Open
Abstract
Baloxavir marboxil (BXM) is an FDA-approved antiviral prodrug for the treatment of influenza A and B infection and postexposure prophylaxis. The active form, baloxavir acid (BXA), targets the cap-snatching endonuclease (PA) of the influenza virus polymerase complex. The nuclease activity delivers the primer for transcription, and previous reports have shown that BXA blocks the nuclease activity with high potency. However, biochemical studies on the mechanism of action are lacking. Structural data have shown that BXA chelates the two divalent metal ions at the active site, like inhibitors of the human immunodeficiency virus type 1 (HIV-1) integrase or ribonuclease (RNase) H. Here we studied the mechanisms underlying the high potency of BXA and how the I38T mutation confers resistance to the drug. Enzyme kinetics with the recombinant heterotrimeric enzyme (FluB-ht) revealed characteristics of a tight binding inhibitor. The apparent inhibitor constant (Kiapp) is 12 nM, while the I38T mutation increased Kiapp by ∼18-fold. Order-of-addition experiments show that a preformed complex of FluB-ht, Mg2+ ions and BXA is required to observe inhibition, which is consistent with active site binding. Conversely, a preformed complex of FluB-ht and RNA substrate prevents BXA from accessing the active site. Unlike integrase inhibitors that interact with the DNA substrate, BXA behaves like RNase H inhibitors that compete with the nucleic acid at the active site. The collective data support the conclusion that BXA is a tight binding inhibitor and the I38T mutation diminishes these properties.
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Affiliation(s)
- Brendan Todd
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada; Li Ka Shing Institute of Virology at University of Alberta, Edmonton, Alberta, Canada.
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20
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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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21
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Li Q, Lomonosova E, Donlin MJ, Cao F, O'Dea A, Milleson B, Berkowitz AJ, Baucom JC, Stasiak JP, Schiavone DV, Abdelmessih RG, Lyubimova A, Fraboni AJ, Bejcek LP, Villa JA, Gallicchio E, Murelli RP, Tavis JE. Amide-containing α-hydroxytropolones as inhibitors of hepatitis B virus replication. Antiviral Res 2020; 177:104777. [PMID: 32217151 PMCID: PMC7199283 DOI: 10.1016/j.antiviral.2020.104777] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 12/19/2022]
Abstract
The Hepatitis B Virus (HBV) ribonuclease H (RNaseH) is a promising but unexploited drug target. Here, we synthesized and analyzed a library of 57 amide-containing α-hydroxytropolones (αHTs) as potential leads for HBV drug development. Fifty percent effective concentrations ranged from 0.31 to 54 μM, with selectivity indexes in cell culture of up to 80. Activity against the HBV RNaseH was confirmed in semi-quantitative enzymatic assays with recombinant HBV RNaseH. The compounds were overall poorly active against human ribonuclease H1, with 50% inhibitory concentrations of 5.1 to >1,000 μM. The αHTs had modest activity against growth of the fungal pathogen Cryptococcus neoformans, but had very limited activity against growth of the Gram - bacterium Escherichia coli and the Gram + bacterium Staphylococcus aureus, indicating substantial selectivity for HBV. A molecular model of the HBV RNaseH templated against the Ty3 RNaseH was generated. Docking the compounds to the RNaseH revealed the anticipated binding pose with the divalent cation coordinating motif on the compounds chelating the two Mn++ ions modeled into the active site. These studies reveal that that amide αHTs can be strong, specific HBV inhibitors that merit further assessment toward becoming anti-HBV drugs.
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Affiliation(s)
- Qilan Li
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 S. Grand Blvd, Saint Louis, MO, 63104, USA
| | - Elena Lomonosova
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 S. Grand Blvd, Saint Louis, MO, 63104, USA.
| | - Maureen J Donlin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1100 S. Grand Blvd, Saint Louis, MO, 63104, USA.
| | - Feng Cao
- John Cochran Division, Department of Veterans Affairs Medical Center, Saint Louis, MO, USA.
| | - Austin O'Dea
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 S. Grand Blvd, Saint Louis, MO, 63104, USA.
| | - Brienna Milleson
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 S. Grand Blvd, Saint Louis, MO, 63104, USA
| | - Alex J Berkowitz
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY, 11210, USA; Program in Chemistry, The Graduate Center of The City University of New York, New York, NY, 11210, USA.
| | - John-Charles Baucom
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY, 11210, USA; Program in Chemistry, The Graduate Center of The City University of New York, New York, NY, 11210, USA.
| | - John P Stasiak
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY, 11210, USA.
| | - Daniel V Schiavone
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY, 11210, USA; Program in Chemistry, The Graduate Center of The City University of New York, New York, NY, 11210, USA.
| | - Rudolf G Abdelmessih
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY, 11210, USA.
| | - Anastasiya Lyubimova
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY, 11210, USA.
| | - Americo J Fraboni
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY, 11210, USA.
| | - Lauren P Bejcek
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY, 11210, USA; Program in Chemistry, The Graduate Center of The City University of New York, New York, NY, 11210, USA.
| | - Juan A Villa
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 S. Grand Blvd, Saint Louis, MO, 63104, USA.
| | - Emilio Gallicchio
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY, 11210, USA; Program in Chemistry, The Graduate Center of The City University of New York, New York, NY, 11210, USA; Program in Biochemistry, The Graduate Center of The City University of New York, New York, NY, 11210, USA.
| | - Ryan P Murelli
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY, 11210, USA; Program in Chemistry, The Graduate Center of The City University of New York, New York, NY, 11210, USA; Program in Biochemistry, The Graduate Center of The City University of New York, New York, NY, 11210, USA.
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, 1100 S. Grand Blvd, Saint Louis, MO, 63104, USA.
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22
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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: 6] [Impact Index Per Article: 1.5] [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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23
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Wang L, Sarafianos SG, Wang Z. Cutting into the Substrate Dominance: Pharmacophore and Structure-Based Approaches toward Inhibiting Human Immunodeficiency Virus Reverse Transcriptase-Associated Ribonuclease H. Acc Chem Res 2020; 53:218-230. [PMID: 31880912 DOI: 10.1021/acs.accounts.9b00450] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Human immunodeficiency virus (HIV) reverse transcriptase (RT) contains two distinct functional domains: a DNA polymerase (pol) domain and a ribonuclease H (RNase H) domain, both of which are required for viral genome replication. Over the last 3 decades, RT has been at the forefront of HIV drug discovery efforts with numerous nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs) approved by the FDA. However, all these RT inhibitors target only the pol function, and inhibitors of RT-associated RNase H have yet to enter the development pipeline, which in itself manifests both the opportunity and challenges of targeting RNase H: if developed, RT RNase H inhibitors would represent a mechanistically novel class of HIV drugs that can be particularly valuable in treating HIV strains resistant to current drugs. The challenges include (1) the difficulty in selectively targeting RT RNase H over RT pol due to their close interplay both spatially and temporally and over HIV-1 integrase strand transfer (INST) activity because of their active site similarities; (2) to a larger extent, the inability of active site inhibitors to confer significant antiviral effect, presumably due to a steep substrate barrier by which the pre-existing substrate prevents access of small molecules to the active site. As a result, previously reported RT RNase H inhibitors typically lacked target specificity and significant antiviral potency. Achieving meaningful antiviral activity via active site targeting likely entails selective and ultrapotent RNase H inhibition to allow small molecules to cut into the dominance of substrates. Based on a pharmacophore model informed by prior work, we designed and redesigned a few metal-chelating chemotypes, such as 2-hydroxyisoquinolinedione (HID), hydroxypyridonecarboxylic acid (HPCA), 3-hydroxypyrimidine-2,4-dione (HPD), and N-hydroxythienopyrimidine-2,4-dione (HTPD). Analogues of these chemotypes generally exhibited improved potency and selectivity inhibiting RT RNase H over the best previous compounds and further validated the pharmacophore model. Extended structure-activity relationship (SAR) on the HPD inhibitor type by mainly altering the linkage generated a few subtypes showing exceptional potency (single-digit nanomolar) and excellent selectivity over the inhibition of RT pol and INST. In parallel, a structure-based approach also allowed us to design a unique double-winged HPD subtype to potently and selectively inhibit RT RNase H and effectively compete against the RNA/DNA substrate. Significantly, all potent HPD subtypes consistently inhibited HIV-1 in the cell culture, suggesting that carefully designed active site RNase H inhibitors with ultrapotency could partially overcome the barrier to antiviral phenotype. Overall, in addition to identifying our own inhibitor types, our medicinal chemistry efforts demonstrated the value of pharmacophore and structure-based approaches in designing active side-directed RNase H inhibitors and could provide a viable path to validating RNase H as a novel antiviral target.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Fine Chemicals, Department of Pharmacy, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
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24
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Lanave G, Martella V, Tempesta M, Catella C, Murelli RP, Morrison LA, Lucente MS, Buonavoglia C, Camero M. Antiviral activity of Α-hydroxytropolones on caprine alphaherpesvirus 1 in vitro. Res Vet Sci 2020; 129:99-102. [PMID: 31954321 DOI: 10.1016/j.rvsc.2020.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/08/2020] [Accepted: 01/10/2020] [Indexed: 11/29/2022]
Abstract
The emergence of human alphaherpesvirus strains (i.e. HHV-1 and -2) resistant to commonly used antiviral drugs has prompted the research for alternative, biologically active anti-herpetic agents. Natural-product and synthetic α-hydroxytropolones (αHTs) have been identified as lead therapeutic agents for a number of infections, including HHV-1 and -2, and several veterinary herpesviruses, i.e. bovine alphaherpesvirus 1 (BoHV-1), equine alphaherpesvirus 1 (EHV-1) and feline alphaherpesvirus 1 (FHV-1). In the present study we evaluated the activity in vitro of two natural and two synthetic α-hydroxytropolones (αHTs) against Caprine alphaherpesvirus 1 (CpHV-1) which is regarded as a useful homologous animal model for the study of HSV-2 infection, chiefly for the assessment of antiviral drugs in in vivo studies. AlphaHTs were able to decrease significantly CpHV-1 viral titres up to 4.25 log10 TCID50/50 μl and suppressed extensively CpHV-1 nucleic acids up to 8.71 log10 viral DNA copy number/10 μl. This study demonstrated the efficacy of αHTs against CpHV-1 in vitro, adding to their activity observed against the human and animal alphaherpesviruses in vitro. The activity of αHTs against CpHV-1 appeared similar but not identical to the patterns of activity observed against other alphaherpesviruses, suggesting virus-related variability in terms of response to specific αHT molecules. These findings open several perspectives in terms of future studies using the CpHV-1 homologous animal model, for the development of therapeutic tools against herpesviruses.
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Affiliation(s)
- Gianvito Lanave
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy.
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
| | - Maria Tempesta
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
| | - Cristiana Catella
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
| | - Ryan P Murelli
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY, USA; The Graduate Center of the City University of New York, New York, NY, USA
| | - Lynda A Morrison
- Departments of Molecular Microbiology and Immunology and of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO, USA
| | | | - Canio Buonavoglia
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
| | - Michele Camero
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy
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25
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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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26
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Watkins EJ, Almhjell PJ, Arnold FH. Direct Enzymatic Synthesis of a Deep-Blue Fluorescent Noncanonical Amino Acid from Azulene and Serine. Chembiochem 2019; 21:80-83. [PMID: 31513332 DOI: 10.1002/cbic.201900497] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Indexed: 12/21/2022]
Abstract
We report a simple, one-step enzymatic synthesis of the blue fluorescent noncanonical amino acid β-(1-azulenyl)-l-alanine (AzAla). By using an engineered tryptophan synthase β-subunit (TrpB), stereochemically pure AzAla can be synthesized at scale starting from commercially available azulene and l-serine. Mutation of a universally conserved catalytic glutamate in the active site to glycine has only a modest effect on native activity with indole but abolishes activity on azulene, suggesting that this glutamate activates azulene for nucleophilic attack by stabilization of the aromatic ion.
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Affiliation(s)
- Ella J Watkins
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Patrick J Almhjell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Frances H Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA.,Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
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27
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Xi Z, Wang Z, Sarafianos SG, Myshakina NS, Ishima R. Determinants of Active-Site Inhibitor Interaction with HIV-1 RNase H. ACS Infect Dis 2019; 5:1963-1974. [PMID: 31577424 DOI: 10.1021/acsinfecdis.9b00300] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The ribonuclease H (RNH) activity of HIV-1 reverse transcriptase (RT) is essential for viral replication and can be a target for drug development. Yet, no RNH inhibitor to date has substantial antiviral activity to allow advancement into clinical development. Herein, we describe our characterization of the detailed binding mechanisms of RNH active-site inhibitors, YLC2-155 and ZW566, that bind to the RNH domain through divalent metal ions, using NMR, molecular docking, and quantum mechanical calculations. In the presence of Mg2+, NMR spectra of RNH exhibited split (two) resonances for some residues upon inhibitor binding, suggesting two binding modes, an observation consistent with the docking results. The relative populations of the two binding conformers were independent of inhibitor or Mg2+ concentration, with one conformation consistently more favored. In our docking study, one distinctive pose of ZW566 showed more interactions with surrounding residues of RNH compared to the analogous binding pose of YLC2-155. Inhibitor titration experiments revealed a lower dissociation constant for ZW566 compared to YLC2-155, in agreement with its higher inhibitory activity. Mg2+ titration data also indicated a stronger dependence on Mg2+ for the RNH interaction with ZW566 compared to YLC2-155. Combined docking and quantum mechanical calculation results suggest that stronger metal coordination as well as more protein-inhibitor interactions may account for the higher binding affinity of ZW566. These findings support the idea that strategies for the development of potent competitive active site RNH inhibitors should take into account not only metal-inhibitor coordination but also protein-inhibitor interaction and conformational selectivity.
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Affiliation(s)
- Zhaoyong Xi
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, 516 Delaware Street SE, PWB 7-215,
MMC 204, Minneapolis, Minnesota 55455, United States
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Nataliya S. Myshakina
- Department of Natural Science, Chatham University, Woodland Road, Pittsburgh, Pennsylvania 15232, United States
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
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28
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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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29
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Edwards TC, Ponzar NL, Tavis JE. Shedding light on RNaseH: a promising target for hepatitis B virus (HBV). Expert Opin Ther Targets 2019; 23:559-563. [PMID: 31084514 DOI: 10.1080/14728222.2019.1619697] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Tiffany C Edwards
- a Department of Molecular Microbiology and Immunology , Saint Louis University Liver Center, Saint Louis University School of Medicine , Saint Louis , MO , USA
| | - Nathan L Ponzar
- a Department of Molecular Microbiology and Immunology , Saint Louis University Liver Center, Saint Louis University School of Medicine , Saint Louis , MO , USA
| | - John E Tavis
- a Department of Molecular Microbiology and Immunology , Saint Louis University Liver Center, Saint Louis University School of Medicine , Saint Louis , MO , USA
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30
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Tang J, Do HT, Huber AD, Casey MC, Kirby KA, Wilson DJ, Kankanala J, Parniak MA, Sarafianos SG, Wang Z. Pharmacophore-based design of novel 3-hydroxypyrimidine-2,4-dione subtypes as inhibitors of HIV reverse transcriptase-associated RNase H: Tolerance of a nonflexible linker. Eur J Med Chem 2019; 166:390-399. [PMID: 30739822 PMCID: PMC6459026 DOI: 10.1016/j.ejmech.2019.01.081] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/17/2019] [Accepted: 01/30/2019] [Indexed: 11/29/2022]
Abstract
The pharmacophore of active site inhibitors of human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H typically entails a flexible linker connecting the chelating core and the hydrophobic aromatics. We report herein that novel 3-hydroxypyrimidine-2,4-dione (HPD) subtypes with a nonflexible C-6 carbonyl linkage exhibited potent and selective biochemical inhibitory profiles with strong RNase H inhibition at low nM, weak to moderate integrase strand transfer (INST) inhibition at low μM, and no to marginal RT polymerase (pol) inhibition up to 10 μM. A few analogues also demonstrated significant antiviral activity without cytotoxicity. The overall inhibitory profile is comparable to or better than that of previous HPD subtypes with a flexible C-6 linker, suggesting that the nonflexible carbonyl linker can be tolerated in the design of novel HIV RNase H active site inhibitors.
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Affiliation(s)
- Jing Tang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ha T Do
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Andrew D Huber
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA
| | - Mary C Casey
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA
| | - Karen A Kirby
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA; Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Daniel J Wilson
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jayakanth Kankanala
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Michael A Parniak
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA; Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA.
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31
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Oda M, Xi Z, Inaba S, Slack RL, Ishima R. Binding thermodynamics of metal ions to HIV-1 ribonuclease H domain. JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY 2019; 135:2647-2653. [PMID: 30853849 PMCID: PMC6402781 DOI: 10.1007/s10973-018-7445-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/27/2018] [Indexed: 06/09/2023]
Abstract
Metal-protein interactions are not necessarily tight in many transient biological processes, such as cellular signaling, enzyme regulation, and molecular recognition. Here, we analyzed the binding thermodynamics and characterized the structural effect of divalent metal ions, i.e. Mn2+, Zn2+, and Mg2+, to the isolated ribonuclease H (RNH) of human immunodeficiency virus (HIV) using isothermal titration calorimetry (ITC) and circular dichroism. The binding thermodynamics of Mg2+ to RNH was determined using competition ITC experiments, and the binding affinity of Mg2+ was found to be about 40- and 400-times lower than those of Mn2+ and of Zn2+, respectively. The structural analysis showed that Mg2+ binding had little effect on the thermal stability of RNH, while Zn2+ and Mn2+ binding increased the stability. The thermodynamic characteristics of RNH metal binding, compared to intact HIV reverse transcriptase, and a possible mechanism of conformational change induced upon metal ion binding, in correlation with the structure-function relationship, are discussed.
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Affiliation(s)
- Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| | - Zhaoyong Xi
- Department of Structural Biology, University of Pittsburgh School of, Medicine, Pittsburgh, Pennsylvania 15260, United States
| | - Satomi Inaba
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
- Research & Utilization Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Ryan L. Slack
- Department of Structural Biology, University of Pittsburgh School of, Medicine, Pittsburgh, Pennsylvania 15260, United States
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of, Medicine, Pittsburgh, Pennsylvania 15260, United States
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32
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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33
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London RE. HIV-1 Reverse Transcriptase: A Metamorphic Protein with Three Stable States. Structure 2019; 27:420-426. [PMID: 30639227 DOI: 10.1016/j.str.2018.11.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/31/2018] [Accepted: 11/27/2018] [Indexed: 11/18/2022]
Abstract
There has been a steadily increasing appreciation of the fact that the relationship between protein sequence and structure is often sufficiently ambiguous to allow a single sequence to adopt alternative, stable folds. Living organisms have been able to utilize such metamorphic proteins in remarkable and unanticipated ways. HIV-1 reverse transcriptase is among the earliest such proteins identified and remains a unique example in which a functional heterodimer contains two, alternatively folded polymerase domains. Structural characterization of the p66 precursor protein combined with NMR spectroscopic and molecular modeling studies have provided insights into the factors underlying the metamorphic transition and the subunit-specific programmed unfolding step required to expose the protease cleavage site within the ribonuclease H domain, supporting the conversion of the p66/p66' precursor into the mature p66/p51 heterodimer.
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Affiliation(s)
- Robert E London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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34
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Gao Y, Chen Y, Tian Y, Zhao Y, Wu F, Luo X, Ju X, Liu G. In silico study of 3-hydroxypyrimidine-2,4-diones as inhibitors of HIV RT-associated RNase H using molecular docking, molecular dynamics, 3D-QSAR, and pharmacophore models. NEW J CHEM 2019. [DOI: 10.1039/c9nj03353j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Rational design and virtual screening of novel inhibitors of HIV reverse transcriptase associated ribonuclease H based on a combined molecular modeling study.
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Affiliation(s)
- Ya Gao
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Yanming Chen
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Yafeng Tian
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Yilan Zhao
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Fengshou Wu
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Xiaogang Luo
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Xiulian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
| | - Genyan Liu
- Key Laboratory for Green Chemical Process of Ministry of Education
- School of Chemical Engineering and Pharmacy
- Wuhan Institute of Technology
- Wuhan 430205
- P. R. China
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35
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Shirvani P, Fassihi A, Saghaie L. Recent Advances in the Design and Development of Non-nucleoside Reverse Transcriptase Inhibitor Scaffolds. ChemMedChem 2018; 14:52-77. [PMID: 30417561 DOI: 10.1002/cmdc.201800577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 11/04/2018] [Indexed: 12/31/2022]
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) have always been an important part of the anti-HIV-1 combination therapy known as combination antiretroviral therapy (cART) since 1996. The use of NNRTIs for about 22 years has led to some mutations in the residues that compose the reverse transcriptase active site, resulting in the emergence of drug-resistant viruses. Thus, the search for new potent NNRTIs with an improved safety profile and activity against drug-resistant HIV strains is indispensable, and many hit and lead NNRTIs have been discovered in the last decade. This review provides an overview of the development in this field from 2013 to August 2018.
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Affiliation(s)
- Pouria Shirvani
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Hezar Jerib Avenue, 81746-73461, Isfahan, Iran
| | - Afshin Fassihi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Hezar Jerib Avenue, 81746-73461, Isfahan, Iran
| | - Lotfollah Saghaie
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Hezar Jerib Avenue, 81746-73461, Isfahan, Iran
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36
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Cao F, Orth C, Donlin MJ, Adegboyega P, Meyers MJ, Murelli RP, Elagawany M, Elgendy B, Tavis JE. Synthesis and Evaluation of Troponoids as a New Class of Antibiotics. ACS OMEGA 2018; 3:15125-15133. [PMID: 30533576 PMCID: PMC6275967 DOI: 10.1021/acsomega.8b01754] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/19/2018] [Indexed: 05/11/2023]
Abstract
Novel antibiotics are urgently needed. The troponoids [tropones, tropolones, and α-hydroxytropolones (α-HT)] can have anti-bacterial activity. We synthesized or purchased 92 troponoids and evaluated their antibacterial activities against Staphylococcus aureus, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa. Preliminary hits were assessed for minimum inhibitory concentrations (MIC80) and cytotoxicity (CC50) against human hepatoma cells. Sixteen troponoids inhibited S. aureus/E. coli/A. baumannii growth by ≥80% growth at <30 μM with CC50 values >50 μM. Two selected tropolones (63 and 285) inhibited 18 methicillin-resistant S. aureus (MRSA) strains with similar MIC80 values as against a reference strain. Two selected thiotropolones (284 and 363) inhibited multidrug-resistant (MDR) E. coli with MIC80 ≤30 μM. One α-HT (261) inhibited MDR-A. baumannii with MIC80 ≤30 μM. This study opens new avenues for development of novel troponoid antibiotics to address the critical need to combat MDR bacterial infections.
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Affiliation(s)
- Feng Cao
- John
Cochran Division, Department of Veterans Affairs Medical Center, 915 North Grand Blvd., St. Louis, Missouri 63106, United States
- E-mail: . Phone: +1 (314) 289-6358. Fax: +1(314) 289-7920 (F.C.)
| | - Cari Orth
- John
Cochran Division, Department of Veterans Affairs Medical Center, 915 North Grand Blvd., St. Louis, Missouri 63106, United States
| | - Maureen J. Donlin
- Edward
A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Patrick Adegboyega
- John
Cochran Division, Department of Veterans Affairs Medical Center, 915 North Grand Blvd., St. Louis, Missouri 63106, United States
| | - Marvin J. Meyers
- Department
of Chemistry, Saint Louis University, St. Louis, Missouri 63104, United States
| | - Ryan P. Murelli
- Department
of Chemistry, Brooklyn College, The City
University of New York, Brooklyn, New York 11210, United States
- PhD
Program in Chemistry, The Graduate Center
of The City University of New York, New York 10016, United
States
| | - Mohamed Elagawany
- Center for
Clinical Pharmacology, Washington University
School of Medicine and St. Louis College of Pharmacy, St. Louis, Missouri 63110, United States
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Damanhour University, Damanhour 31111, Egypt
| | - Bahaa Elgendy
- Center for
Clinical Pharmacology, Washington University
School of Medicine and St. Louis College of Pharmacy, St. Louis, Missouri 63110, United States
- Chemistry
Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - John E. Tavis
- Department
of Molecular Microbiology and Immunology, The Saint Louis University Liver Center, Saint Louis University School
of Medicine, St. Louis, Missouri 63104, United
States
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37
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Elagawany M, Hegazy L, Cao F, Donlin MJ, Rath N, Tavis J, Elgendy B. Identification of 4-isopropyl-thiotropolone as a novel anti-microbial: regioselective synthesis, NMR characterization, and biological evaluation. RSC Adv 2018; 8:29967-29975. [PMID: 35547306 PMCID: PMC9085298 DOI: 10.1039/c8ra06297h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/20/2018] [Indexed: 12/30/2022] Open
Abstract
We have synthesized and separated tosylated thujaplicin isomers for the first time, and elucidated their structures using 1D, 2D-NMR techniques and X-ray crystallography. The tosylated isomers were used to synthesize 4-isopropyl–thiotropolone and 6-isopropyl–thiotropolone in a regioselective manner. 1H and 13C Chemical shifts of synthesized isomers were fully assigned using several NMR experiments, and their isotropic magnetic shielding was calculated using the GIAO (Gauge Including Atomic Orbitals) method and the B3LYP def2-TZVPP level of theory. The calculated chemical shift values were in a good agreement with the experimental results. The biological activity of all synthesized compounds was evaluated against the fungal pathogen Cryptococcus neoformans and four different bacterial strains (Staphylococcus aureus (ATCC 29213), E. coli (ATCC 35218), Acinetobacter baumannii and Pseudomonas aeruginosa (ATCC 27853)). 4-Isopropyl–thiotropolone was found to inhibit Staphylococcus aureus in a low micro molar range and exhibit good therapeutic index and ADME properties. This compound can be used for future lead optimization to design inhibitors against Staphylococcus aureus (ATCC 29213). 4-Isopropyl–thiotropolone was identified as a novel anti-microbial agent with good therapeutic index and ADME properties.![]()
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Affiliation(s)
- Mohamed Elagawany
- Departments of Pharmacology and Physiology, Saint Louis University School of Medicine St. Louis MO USA.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Damanhour University Damanhour Egypt
| | - Lamees Hegazy
- Departments of Pharmacology and Physiology, Saint Louis University School of Medicine St. Louis MO USA
| | - Feng Cao
- John Cochran Division, Department of Veteran's Affairs Medical Center 915 North Grand Blvd. St. Louis MO 63106 USA
| | - Maureen J Donlin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine St. Louis Missouri USA
| | - Nigam Rath
- Department of Chemistry and Biochemistry, Center for Nanoscience, University of Missouri - St. Louis One University Boulevard St. Louis USA
| | - John Tavis
- Department of Molecular Microbiology and Immunology, The Saint Louis University Liver Center, Saint Louis University School of Medicine St. Louis Missouri USA
| | - Bahaa Elgendy
- Departments of Pharmacology and Physiology, Saint Louis University School of Medicine St. Louis MO USA.,Chemistry Department, Faculty of Science, Benha University Benha 13518 Egypt
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38
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Wang L, Tang J, Huber AD, Casey MC, Kirby KA, Wilson DJ, Kankanala J, Parniak MA, Sarafianos SG, Wang Z. 6-Biphenylmethyl-3-hydroxypyrimidine-2,4-diones potently and selectively inhibited HIV reverse transcriptase-associated RNase H. Eur J Med Chem 2018; 156:680-691. [PMID: 30031978 DOI: 10.1016/j.ejmech.2018.07.035] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/11/2018] [Accepted: 07/14/2018] [Indexed: 12/11/2022]
Abstract
Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated ribonuclease H (RNase H) remains an unvalidated drug target. Reported HIV RNase H inhibitors generally lack significant antiviral activity. We report herein the design, synthesis, biochemical and antiviral evaluations of a new 6-biphenylmethyl subtype of the 3-hydroxypyrimidine-2,4-dione (HPD) chemotype. In biochemical assays, analogues of this new subtype potently inhibited RT RNase H in low nanomolar range without inhibiting RT polymerase (pol) or integrase strand transfer (INST) at the highest concentrations tested. In cell-based assays, a few analogues inhibited HIV in low micromolar range without cytotoxicity at concentrations up to 100 μM.
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Affiliation(s)
- Lei Wang
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jing Tang
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Andrew D Huber
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Mary C Casey
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - Karen A Kirby
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA; Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Daniel J Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jayakanth Kankanala
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael A Parniak
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA; Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Zhengqiang Wang
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA.
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39
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Wang L, Tang J, Huber AD, Casey MC, Kirby KA, Wilson DJ, Kankanala J, Xie J, Parniak MA, Sarafianos SG, Wang Z. 6-Arylthio-3-hydroxypyrimidine-2,4-diones potently inhibited HIV reverse transcriptase-associated RNase H with antiviral activity. Eur J Med Chem 2018; 156:652-665. [PMID: 30031976 DOI: 10.1016/j.ejmech.2018.07.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 05/31/2018] [Accepted: 07/15/2018] [Indexed: 12/17/2022]
Abstract
Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) remains the only virally encoded enzymatic function not targeted by current drugs. Although a few chemotypes have been reported to inhibit HIV RNase H in biochemical assays, their general lack of significant antiviral activity in cell culture necessitates continued efforts in identifying highly potent RNase H inhibitors to confer antiviral activity. We report herein the design, synthesis, biochemical and antiviral evaluations of a new 6-arylthio subtype of the 3-hydroxypyrimidine-2,4-dione (HPD) chemotype. In biochemical assays these new analogues inhibited RT RNase H in single-digit nanomolar range without inhibiting RT polymerase (pol) at concentrations up to 10 μM, amounting to exceptional biochemical inhibitory selectivity. Many analogues also inhibited integrase strand transfer (INST) activity in low to sub micromolar range. More importantly, most analogues inhibited HIV in low micromolar range without cytotoxicity. In the end, compound 13j (RNase H IC50 = 0.005 μM; RT pol IC50 = 10 μM; INST IC50 = 4.0 μM; antiviral EC50 = 7.7 μM; CC50 > 100 μM) represents the best analogues within this series. These results characterize the new 6-arylthio-HPD subtype as a promising scaffold for HIV RNase H inhibitor discovery.
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Affiliation(s)
- Lei Wang
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jing Tang
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Andrew D Huber
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA
| | - Mary C Casey
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA
| | - Karen A Kirby
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA; Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Daniel J Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jayakanth Kankanala
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jiashu Xie
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Michael A Parniak
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA; Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Department of Biochemistry, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA
| | - Zhengqiang Wang
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA.
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40
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Developing and Evaluating Inhibitors against the RNase H Active Site of HIV-1 Reverse Transcriptase. J Virol 2018; 92:JVI.02203-17. [PMID: 29643235 DOI: 10.1128/jvi.02203-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/31/2018] [Indexed: 12/25/2022] Open
Abstract
We tested three compounds for their ability to inhibit the RNase H (RH) and polymerase activities of HIV-1 reverse transcriptase (RT). A high-resolution crystal structure (2.2 Å) of one of the compounds showed that it chelates the two magnesium ions at the RH active site; this prevents the RH active site from interacting with, and cleaving, the RNA strand of an RNA-DNA heteroduplex. The compounds were tested using a variety of substrates: all three compounds inhibited the polymerase-independent RH activity of HIV-1 RT. Time-of-addition experiments showed that the compounds were more potent if they were bound to RT before the nucleic acid substrate was added. The compounds significantly inhibited the site-specific cleavage required to generate the polypurine tract (PPT) RNA primer that initiates the second strand of viral DNA synthesis. The compounds also reduced the polymerase activity of RT; this ability was a result of the compounds binding to the RH active site. These compounds appear to be relatively specific; they do not inhibit either Escherichia coli RNase HI or human RNase H2. The compounds inhibit the replication of an HIV-1-based vector in a one-round assay, and their potencies were only modestly decreased by mutations that confer resistance to integrase strand transfer inhibitors (INSTIs), nucleoside analogs, or nonnucleoside RT inhibitors (NNRTIs), suggesting that their ability to block HIV replication is related to their ability to block RH cleavage. These compounds appear to be useful leads that can be used to develop more potent and specific compounds.IMPORTANCE Despite advances in HIV-1 treatment, drug resistance is still a problem. Of the four enzymatic activities found in HIV-1 proteins (protease, RT polymerase, RT RNase H, and integrase), only RNase H has no approved therapeutics directed against it. This new target could be used to design and develop new classes of inhibitors that would suppress the replication of the drug-resistant variants that have been selected by the current therapeutics.
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41
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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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42
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Abstract
α-Hydroxytropolones (αHTs) are troponoids that demonstrate inhibition against an array of therapeutically significant targets, making them potential drug leads for several human diseases. We have utilized a recently discovered one-pot three-component oxidopyrylium cycloaddition in a solid-supported synthesis of αHTs. Though the procedure is time efficient and generates assay-ready molecules, the system suffers from low yields and an inability to perform reaction modifications on resin-bound intermediates. In order to combat these issues with the solid-phase platform, we incorporated fluorous tags into our synthetic route. Through the implementation of fluorous phase chemistry, we demonstrate a substantial increase in the overall yield of αHTs, as well as an ability to execute metal-catalyzed cross coupling and amide coupling on fluorous tagged intermediates. We also show that tagged molecules can be separated from nonfluorous impurities, and vice versa, by utilizing fluorous liquid-liquid and solid-phase extractions. Hence, these proof-of-principle investigations describe the viability of a fluorous phase approach to αHT synthesis and its potential to serve as a combinatorial technique to produce structurally diverse substrates.
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Affiliation(s)
- Michael P. D’Erasmo
- Department of Chemistry, Brooklyn College, The City
University of New York, Brooklyn, New York 11210, United States
- PhD Program in Chemistry, The Graduate Center of The City
University of New York, New York, New York 10016, United States
| | - Ryan P. Murelli
- Department of Chemistry, Brooklyn College, The City
University of New York, Brooklyn, New York 11210, United States
- PhD Program in Chemistry, The Graduate Center of The City
University of New York, New York, New York 10016, United States
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43
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Hirsch DR, Schiavone DV, Berkowitz AJ, Morrison LA, Masaoka T, Wilson JA, Lomonosova E, Zhao H, Patel BS, Datla SH, Hoft SG, Majidi SJ, Pal RK, Gallicchio E, Tang L, Tavis JE, Le Grice SFJ, Beutler JA, Murelli RP. Synthesis and biological assessment of 3,7-dihydroxytropolones. Org Biomol Chem 2017; 16:62-69. [PMID: 29098212 PMCID: PMC5748270 DOI: 10.1039/c7ob02453c] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
3,7-Dihydroxytropolones (3,7-dHTs) are highly oxygenated troponoids that have been identified as lead compounds for several human diseases. To date, structure-function studies on these molecules have been limited due to a scarcity of synthetic methods for their preparation. New synthetic strategies towards structurally novel 3,7-dHTs would be valuable in further studying their therapeutic potential. Here we describe the successful adaptation of a [5 + 2] oxidopyrilium cycloaddition/ring-opening for 3,7-dHT synthesis, which we apply in the synthesis of a plausible biosynthetic intermediate to the natural products puberulic and puberulonic acid. We have also tested these new compounds in several biological assays related to human immunodeficiency virus (HIV), hepatitis B virus (HBV) and herpes simplex virus (HSV) in order to gain insight into structure-functional analysis related to antiviral troponoid development.
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Affiliation(s)
- D R Hirsch
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, New York, 11210, USA.
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44
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Kankanala J, Kirby KA, Huber AD, Casey MC, Wilson DJ, Sarafianos SG, Wang Z. Design, synthesis and biological evaluations of N-Hydroxy thienopyrimidine-2,4-diones as inhibitors of HIV reverse transcriptase-associated RNase H. Eur J Med Chem 2017; 141:149-161. [PMID: 29031062 DOI: 10.1016/j.ejmech.2017.09.054] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/13/2017] [Accepted: 09/25/2017] [Indexed: 11/29/2022]
Abstract
Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) is the only HIV enzymatic function not targeted by current antiviral drugs. Although various chemotypes have been reported to inhibit HIV RNase H, few have shown significant antiviral activities. We report herein the design, synthesis and biological evaluation of a novel N-hydroxy thienopyrimidine-2,3-dione chemotype (11) which potently and selectively inhibited RNase H with considerable potency against HIV-1 in cell culture. Current structure-activity-relationship (SAR) identified analogue 11d as a nanomolar inhibitor of RNase H (IC50 = 0.04 μM) with decent antiviral potency (EC50 = 7.4 μM) and no cytotoxicity (CC50 > 100 μM). In extended biochemical assays compound 11d did not inhibit RT polymerase (pol) while inhibiting integrase strand transfer (INST) with 53 fold lower potency (IC50 = 2.1 μM) than RNase H inhibition. Crystallographic and molecular modeling studies confirmed the RNase H active site binding mode.
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Affiliation(s)
- Jayakanth Kankanala
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Karen A Kirby
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Andrew D Huber
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Mary C Casey
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Daniel J Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stefan G Sarafianos
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA; Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Zhengqiang Wang
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA.
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45
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A 2-Hydroxyisoquinoline-1,3-Dione Active-Site RNase H Inhibitor Binds in Multiple Modes to HIV-1 Reverse Transcriptase. Antimicrob Agents Chemother 2017; 61:AAC.01351-17. [PMID: 28760905 DOI: 10.1128/aac.01351-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/07/2017] [Indexed: 11/20/2022] Open
Abstract
The RNase H (RNH) function of HIV-1 reverse transcriptase (RT) plays an essential part in the viral life cycle. We report the characterization of YLC2-155, a 2-hydroxyisoquinoline-1,3-dione (HID)-based active-site RNH inhibitor. YLC2-155 inhibits both polymerase (50% inhibitory concentration [IC50] = 2.6 μM) and RNH functions (IC50 = 0.65 μM) of RT but is more effective against RNH. X-ray crystallography, nuclear magnetic resonance (NMR) analysis, and molecular modeling were used to show that YLC2-155 binds at the RNH-active site in multiple conformations.
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46
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Vernekar SKV, Tang J, Wu B, Huber AD, Casey MC, Myshakina N, Wilson DJ, Kankanala J, Kirby KA, Parniak MA, Sarafianos SG, Wang Z. Double-Winged 3-Hydroxypyrimidine-2,4-diones: Potent and Selective Inhibition against HIV-1 RNase H with Significant Antiviral Activity. J Med Chem 2017; 60:5045-5056. [PMID: 28525279 DOI: 10.1021/acs.jmedchem.7b00440] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated ribonuclease H (RNase H) remains the only virally encoded enzymatic function yet to be exploited as an antiviral target. One of the possible challenges may be that targeting HIV RNase H is confronted with a steep substrate barrier. We have previously reported a 3-hydroxypyrimidine-2,4-dione (HPD) subtype that potently and selectively inhibited RNase H without inhibiting HIV in cell culture. We report herein a critical redesign of the HPD chemotype featuring an additional wing at the C5 position that led to drastically improved RNase H inhibition and significant antiviral activity. Structure-activity relationship (SAR) concerning primarily the length and flexibility of the two wings revealed important structural features that dictate the potency and selectivity of RNase H inhibition as well as the observed antiviral activity. Our current medicinal chemistry data also revealed that the RNase H biochemical inhibition largely correlated the antiviral activity.
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Affiliation(s)
- Sanjeev Kumar V Vernekar
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Jing Tang
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Bulan Wu
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Andrew D Huber
- Department of Veterinary Pathobiology, Christopher S. Bond Life Sciences Center, University of Missouri , Columbia, Missouri 65211, United States
| | - Mary C Casey
- Department of Molecular Microbiology and Immunology, Christopher S. Bond Life Sciences Center, University of Missouri School of Medicine , Columbia, Missouri 65211, United States
| | - Nataliya Myshakina
- Department of Natural Science, Chatham University , 1 Woodland Road, Pittsburgh, Pennsylvania 15232, United States
| | - Daniel J Wilson
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Jayakanth Kankanala
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Karen A Kirby
- Department of Molecular Microbiology and Immunology, Christopher S. Bond Life Sciences Center, University of Missouri School of Medicine , Columbia, Missouri 65211, United States
| | - Michael A Parniak
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15219, United States
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology, Christopher S. Bond Life Sciences Center, University of Missouri School of Medicine , Columbia, Missouri 65211, United States.,Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States
| | - Zhengqiang Wang
- Center for Drug Design, Academic Health Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
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47
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Edwards TC, Lomonosova E, Patel JA, Li Q, Villa JA, Gupta AK, Morrison LA, Bailly F, Cotelle P, Giannakopoulou E, Zoidis G, Tavis JE. Inhibition of hepatitis B virus replication by N-hydroxyisoquinolinediones and related polyoxygenated heterocycles. Antiviral Res 2017; 143:205-217. [PMID: 28450058 DOI: 10.1016/j.antiviral.2017.04.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/06/2017] [Accepted: 04/22/2017] [Indexed: 12/16/2022]
Abstract
We previously reported low sensitivity of the hepatitis B virus (HBV) ribonuclease H (RNaseH) enzyme to inhibition by N-hydroxyisoquinolinedione (HID) compounds. Subsequently, our biochemical RNaseH assay was found to have a high false negative rate for predicting HBV replication inhibition, leading to underestimation of the number of HIDs that inhibit HBV replication. Here, 39 HID compounds and structurally related polyoxygenated heterocycles (POH), N-hydroxypyridinediones (HPD), and flutimides were screened for inhibition of HBV replication in vitro. Inhibiting the HBV RNaseH preferentially blocks synthesis of the positive-polarity DNA strand and causes accumulation of RNA:DNA heteroduplexes. Eleven HIDs and one HPD preferentially inhibited HBV positive-polarity DNA strand accumulation. EC50s ranged from 0.69 μM to 19 μM with therapeutic indices from 2.4 to 71. Neither the HIDs nor the HPD had an effect on the ability of the polymerase to elongate DNA strands in capsids. HBV RNaseH inhibition by the HIDs was confirmed with an improved RNaseH assay and by detecting accumulation RNA:DNA heteroduplexes in HBV capsids from cells treated with a representative HID. Therefore, the HID scaffold is more promising for anti-HBV drug discovery than we originally reported, and the HPD scaffold may hold potential for antiviral development. The preliminary structure-activity relationship will guide optimization of the HID/HPDs as HBV inhibitors.
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Affiliation(s)
- Tiffany C Edwards
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA; Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
| | - Elena Lomonosova
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA; Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
| | - Jenny A Patel
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
| | - Qilan Li
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA; Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
| | - Juan A Villa
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA; Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
| | - Ankit K Gupta
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
| | - Lynda A Morrison
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
| | - Fabrice Bailly
- University of Lille, INSERM, UMR-S 1172, Jean-Pierre Aubert Research Center, Lille, France.
| | - Philippe Cotelle
- University of Lille, INSERM, UMR-S 1172, Jean-Pierre Aubert Research Center, Lille, France.
| | - Erofili Giannakopoulou
- School of Health Sciences, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Athens, Greece.
| | - Grigoris Zoidis
- School of Health Sciences, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Athens, Greece.
| | - John E Tavis
- Department of Molecular Microbiology and Immunology and Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA; Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO, USA.
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48
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An end-point method based on graphene oxide for RNase H analysis and inhibitors screening. Biosens Bioelectron 2016; 90:103-109. [PMID: 27886596 DOI: 10.1016/j.bios.2016.11.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/03/2016] [Accepted: 11/12/2016] [Indexed: 12/12/2022]
Abstract
As a highly conserved damage repair protein, RNase H can hydrolysis DNA-RNA heteroduplex endonucleolytically and cleave RNA-DNA junctions as well. In this study, we have developed an accurate and sensitive RNase H assay based on fluorophore-labeled chimeric substrate hydrolysis and the differential affinity of graphene oxide on RNA strand with different length. This end-point measurement method can detect RNase H in a range of 0.01 to 1 units /mL with a detection limit of 5.0×10-3 units/ mL under optimal conditions. We demonstrate the utility of the assay by screening antibiotics, resulting in the identification of gentamycin, streptomycin and kanamycin as inhibitors with IC50 of 60±5µM, 70±8µM and 300±20µM, respectively. Furthermore, the assay was reliably used to detect RNase H in complicated biosamples and found that RNase H activity in tumor cells was inhibited by gentamycin and streptomycin sulfate in a concentration-dependent manner. The average level of RNase H in serums of HBV infection group was similar to that of control group. In summary, the assay provides an alternative tool for biochemical analysis for this enzyme and indicates the feasibility of high throughput screening inhibitors of RNase H in vitro and in vivo.
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49
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Meleddu R, Distinto S, Corona A, Tramontano E, Bianco G, Melis C, Cottiglia F, Maccioni E. Isatin thiazoline hybrids as dual inhibitors of HIV-1 reverse transcriptase. J Enzyme Inhib Med Chem 2016; 32:130-136. [PMID: 27766892 PMCID: PMC6010014 DOI: 10.1080/14756366.2016.1238366] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A series of 3-3-{2-[2-3-methyl-4-phenyl-2,3-dihydro-1,3-thiazol-2-ylidene]hydrazin-1-ylidene-2,3-dihydro-1H-indol-2-one derivatives has been designed and synthesized to study their activity on both HIV-1 (Human Immunodeficiency Virus type 1) RT (Reverse Transcriptase) associated functions. These derivatives are analogs of previously reported series whose biological activity and mode of action have been investigated. In this work we investigated the influence of the introduction of a methyl group in the position 3 of the dihydrothiazole ring and of a chlorine atom in the position 5 of the isatin nucleus. The new synthesized compounds are active towards both DNA polymerase and ribonuclease H in the µM range. The nature of the aromatic group in the position 4 of the thiazole was relevant in determining the biological activity.
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Affiliation(s)
- Rita Meleddu
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Simona Distinto
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Angela Corona
- b Department of Life and Environmental Sciences , University of Cagliari, Cittadella Universitaria di Monserrato , Cagliari , Italy
| | - Enzo Tramontano
- b Department of Life and Environmental Sciences , University of Cagliari, Cittadella Universitaria di Monserrato , Cagliari , Italy
| | - Giulia Bianco
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Claudia Melis
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Filippo Cottiglia
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
| | - Elias Maccioni
- a Department of Life and Environmental Sciences , University of Cagliari , Cagliari , Italy
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50
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Zhang B, D’Erasmo M, Murelli RP, Gallicchio E. Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase. ACS OMEGA 2016; 1:435-447. [PMID: 27713931 PMCID: PMC5046171 DOI: 10.1021/acsomega.6b00123] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/07/2016] [Indexed: 06/06/2023]
Abstract
We report the results of a binding free energy-based virtual screening campaign of a library of 77 α-hydroxytropolone derivatives against the challenging RNase H active site of the reverse transcriptase (RT) enzyme of human immunodeficiency virus-1. Multiple protonation states, rotamer states, and binding modalities of each compound were individually evaluated. The work involved more than 300 individual absolute alchemical binding free energy parallel molecular dynamics calculations and over 1 million CPU hours on national computing clusters and a local campus computational grid. The thermodynamic and structural measures obtained in this work rationalize a series of characteristics of this system useful for guiding future synthetic and biochemical efforts. The free energy model identified key ligand-dependent entropic and conformational reorganization processes difficult to capture using standard docking and scoring approaches. Binding free energy-based optimization of the lead compounds emerging from the virtual screen has yielded four compounds with very favorable binding properties, which will be the subject of further experimental investigations. This work is one of the few reported applications of advanced-binding free energy models to large-scale virtual screening and optimization projects. It further demonstrates that, with suitable algorithms and automation, advanced-binding free energy models can have a useful role in early-stage drug-discovery programs.
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Affiliation(s)
- Baofeng Zhang
- Department
of Chemistry, Brooklyn
College, City University of New York, Brooklyn, New York 11210, United States
| | - Michael
P. D’Erasmo
- Department
of Chemistry, Brooklyn
College, City University of New York, Brooklyn, New York 11210, United States
- Ph.D. Program in Chemistry and Ph.D. Program in
Biochemistry, The Graduate Center of the
City University of New York, New
York, New York 10016, United States
| | - Ryan P. Murelli
- Department
of Chemistry, Brooklyn
College, City University of New York, Brooklyn, New York 11210, United States
- Ph.D. Program in Chemistry and Ph.D. Program in
Biochemistry, The Graduate Center of the
City University of New York, New
York, New York 10016, United States
| | - Emilio Gallicchio
- Department
of Chemistry, Brooklyn
College, City University of New York, Brooklyn, New York 11210, United States
- Ph.D. Program in Chemistry and Ph.D. Program in
Biochemistry, The Graduate Center of the
City University of New York, New
York, New York 10016, United States
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