1
|
Zhu XD, Corona A, Maloccu S, Tramontano E, Wang S, Pannecouque C, De Clercq E, Meng G, Chen FE. Structure-Based Design of Novel Thiazolone[3,2- a]pyrimidine Derivatives as Potent RNase H Inhibitors for HIV Therapy. Molecules 2024; 29:2120. [PMID: 38731613 PMCID: PMC11085872 DOI: 10.3390/molecules29092120] [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: 03/28/2024] [Revised: 04/20/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Ribonuclease H (RNase H) was identified as an important target for HIV therapy. Currently, no RNase H inhibitors have reached clinical status. Herein, a series of novel thiazolone[3,2-a]pyrimidine-containing RNase H inhibitors were developed, based on the hit compound 10i, identified from screening our in-house compound library. Some of these derivatives exhibited low micromolar inhibitory activity. Among them, compound 12b was identified as the most potent inhibitor of RNase H (IC50 = 2.98 μM). The experiment of magnesium ion coordination was performed to verify that this ligand could coordinate with magnesium ions, indicating its binding ability to the catalytic site of RNase H. Docking studies revealed the main interactions of this ligand with RNase H. A quantitative structure activity relationship (QSAR) was also conducted to disclose several predictive mathematic models. A molecular dynamics simulation was also conducted to determine the stability of the complex. Taken together, thiazolone[3,2-a]pyrimidine can be regarded as a potential scaffold for the further development of RNase H inhibitors.
Collapse
Affiliation(s)
- Xuan-De Zhu
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China; (X.-D.Z.); (S.W.)
| | - Angela Corona
- Department of Life and Environmental Sciences, Department of Applied Science Biosyst, University of Cagliari, 09042 Cagliari, Italy; (A.C.); (S.M.); (E.T.)
| | - Stefania Maloccu
- Department of Life and Environmental Sciences, Department of Applied Science Biosyst, University of Cagliari, 09042 Cagliari, Italy; (A.C.); (S.M.); (E.T.)
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, Department of Applied Science Biosyst, University of Cagliari, 09042 Cagliari, Italy; (A.C.); (S.M.); (E.T.)
| | - Shuai Wang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China; (X.-D.Z.); (S.W.)
| | - Christophe Pannecouque
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium; (C.P.); (E.D.C.)
| | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium; (C.P.); (E.D.C.)
| | - Ge Meng
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China; (X.-D.Z.); (S.W.)
| | - Fen-Er Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China; (X.-D.Z.); (S.W.)
| |
Collapse
|
2
|
Borgelt L, Wu P. Targeting Ribonucleases with Small Molecules and Bifunctional Molecules. ACS Chem Biol 2023; 18:2101-2113. [PMID: 37382390 PMCID: PMC10594538 DOI: 10.1021/acschembio.3c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023]
Abstract
Ribonucleases (RNases) cleave and process RNAs, thereby regulating the biogenesis, metabolism, and degradation of coding and noncoding RNAs. Thus, small molecules targeting RNases have the potential to perturb RNA biology, and RNases have been studied as therapeutic targets of antibiotics, antivirals, and agents for autoimmune diseases and cancers. Additionally, the recent advances in chemically induced proximity approaches have led to the discovery of bifunctional molecules that target RNases to achieve RNA degradation or inhibit RNA processing. Here, we summarize the efforts that have been made to discover small-molecule inhibitors and activators targeting bacterial, viral, and human RNases. We also highlight the emerging examples of RNase-targeting bifunctional molecules and discuss the trends in developing such molecules for both biological and therapeutic applications.
Collapse
Affiliation(s)
- Lydia Borgelt
- Chemical Genomics Centre, Max
Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, Dortmund 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, Dortmund 44227, Germany
| | | |
Collapse
|
3
|
Kang JX, Zhao GK, Yang XM, Huang MX, Hui WQ, Zeng R, Ouyang Q. Recent advances on dual inhibitors targeting HIV reverse transcriptase associated polymerase and ribonuclease H. Eur J Med Chem 2023; 250:115196. [PMID: 36787657 DOI: 10.1016/j.ejmech.2023.115196] [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: 11/15/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
Reverse transcriptase (RT) plays an indispensable role in the replication of human immunodeficiency virus (HIV) through its associated polymerase and ribonuclease H (RNase H) activities during the viral RNA genome transformation into proviral DNA. Due to the fact that HIV is a highly mutagenic virus and easily resistant to single-target RT inhibitors, dual inhibitors targeting HIV RT associated polymerase and RNase H have been developed. These dual inhibitors have the advantages of increasing efficacy, reducing drug resistance, drug-drug interactions, and cytotoxicity, as well as improving patient compliance. In this review, we summarize recent advances in polymerase/RNase H dual inhibitors focusing on drug design strategies, and structure-activity relationships and share new insights into developing anti-HIV drugs.
Collapse
Affiliation(s)
- Jia-Xiong Kang
- Department of Pharmacy, Armed Police Forces Hospital of Sichuan, 614000, Leshan, China
| | - Guang-Kuan Zhao
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Xiu-Ming Yang
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Mou-Xin Huang
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Wen-Qi Hui
- Department of Pharmacy, Xi'an Fifth Hospital, Xian, 710082, Shaanxi, China
| | - Rong Zeng
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China
| | - Qin Ouyang
- Department of Medicinal Chemistry, School of Pharmacy, Third Military Medical University, 400038, Chongqing, China.
| |
Collapse
|
4
|
Temereanca A, Ruta S. Strategies to overcome HIV drug resistance-current and future perspectives. Front Microbiol 2023; 14:1133407. [PMID: 36876064 PMCID: PMC9978142 DOI: 10.3389/fmicb.2023.1133407] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
The availability of combined antiretroviral therapy (cART) has revolutionized the course of HIV infection, suppressing HIV viremia, restoring the immune system, and improving the quality of life of HIV infected patients. However, the emergence of drug resistant and multidrug resistant strains remains an important contributor to cART failure, associated with a higher risk of HIV-disease progression and mortality. According to the latest WHO HIV Drug Resistance Report, the prevalence of acquired and transmitted HIV drug resistance in ART naive individuals has exponentially increased in the recent years, being an important obstacle in ending HIV-1 epidemic as a public health threat by 2030. The prevalence of three and four-class resistance is estimated to range from 5 to 10% in Europe and less than 3% in North America. The new drug development strategies are focused on improved safety and resistance profile within the existing antiretroviral classes, discovery of drugs with novel mechanisms of action (e.g., attachment/post-attachment inhibitors, capsid inhibitors, maturation inhibitors, nucleoside reverse transcriptase translocation inhibitors), combination therapies with improved adherence, and treatment simplification with infrequent dosing. This review highlight the current progress in the management of salvage therapy for patients with multidrug-resistant HIV-1 infection, discussing the recently approved and under development antiretroviral agents, as well as the new drug targets that are providing a new avenue for the development of therapeutic interventions in HIV infection.
Collapse
Affiliation(s)
- Aura Temereanca
- Virology Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Viral Emerging Diseases Department, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Simona Ruta
- Virology Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,Viral Emerging Diseases Department, Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| |
Collapse
|
5
|
He T, Edwards TC, Majima R, Jung E, Kankanala J, Xie J, Geraghty RJ, Wang Z. Repurposing N-hydroxy thienopyrimidine-2,4-diones (HtPD) as inhibitors of human cytomegalovirus pUL89 endonuclease: Synthesis and biological characterization. Bioorg Chem 2022; 129:106198. [PMID: 36265353 PMCID: PMC9643671 DOI: 10.1016/j.bioorg.2022.106198] [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: 08/29/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/02/2022]
Abstract
The terminase complex of human cytomegalovirus (HCMV) is required for viral genome packaging and cleavage. Critical to the terminase functions is a metal-dependent endonuclease at the C-terminus of pUL89 (pUL89-C). We have previously reported metal-chelating N-hydroxy thienopyrimidine-2,4-diones (HtPD) as inhibitors of human immunodeficiency virus 1 (HIV-1) RNase H. In the current work, we have synthesized new analogs and resynthesized known analogs of two isomeric HtPD subtypes, anti-HtPD (13), and syn-HtPD (14), and characterized them as inhibitors of pUL89-C. Remarkably, the vast majority of analogs strongly inhibited pUL89-C in the biochemical endonuclease assay, with IC50 values in the nM range. In the cell-based antiviral assay, a few analogs inhibited HCMV in low μM concentrations. Selected analogs were further characterized in a biophysical thermal shift assay (TSA) and in silico molecular docking, and the results support pUL89-C as the protein target of these inhibitors. Collectively, the biochemical, antiviral, biophysical, and in silico data reported herein indicate that the isomeric HtPD chemotypes 13-14 can serve as valuable chemical platforms for designing improved inhibitors of HCMV pUL89-C.
Collapse
Affiliation(s)
- Tianyu He
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tiffany C Edwards
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ryuichi Majima
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Eunkyung Jung
- 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
| | - Jiashu Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert J Geraghty
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA.
| |
Collapse
|
6
|
Deng C, Yan H, Wang J, Liu K, Liu BS, Shi YM. Current scenario on non-nucleoside reverse transcriptase inhibitors (2018-present). ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
|
7
|
Current medicinal chemistry strategies in the discovery of novel HIV-1 ribonuclease H inhibitors. Eur J Med Chem 2022; 243:114760. [PMID: 36152387 DOI: 10.1016/j.ejmech.2022.114760] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 09/06/2022] [Indexed: 11/23/2022]
Abstract
During HIV-1 genome replication, the viral reverse transcriptase-associated ribonuclease H (RT-associated RNase H) activity hydrolyzes the RNA strand of RNA/DNA heteroduplex intermediates. As of today, HIV-1 RNase H inhibitors (RHIs) remain at an investigational level, although none of them reached clinical trials. Therefore, RNase H remains as an attractive target for drug design and development. In this paper, we review the current status of medicinal chemistry strategies aimed at the discovery of novel RHIs, while discussing problems encountered in their characterization and further development, thereby providing an update on recent progress in the field.
Collapse
|
8
|
Si X, Gao C, Chi L, Wang H, Zhang Y, Dai H, Liu L, Wang Z, Zheng J, Ke Y, Liu H, Zhang Q. Synthesis and in vitro antitumor activity evaluation of novel 5-cyano-6-phenyl-2,4-disubstituted-pyrimidine derivatives. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02950-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
|
9
|
Jung E, Majima R, Edwards TC, Soto-Acosta R, Geraghty RJ, Wang Z. 8-Hydroxy-1,6-naphthyridine-7-carboxamides as Inhibitors of Human Cytomegalovirus pUL89 Endonuclease. ChemMedChem 2022; 17:e202200334. [PMID: 35879245 PMCID: PMC9463105 DOI: 10.1002/cmdc.202200334] [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: 06/20/2022] [Indexed: 11/10/2022]
Abstract
Human cytomegalovirus (HCMV) replication requires a metal-dependent endonuclease at the C-terminus of pUL89 (pUL89-C) for viral genome packaging and cleavage. We have previously shown that pUL89-C can be pharmacologically inhibited with designed metal-chelating compounds. We report herein the synthesis of a few 8-hydroxy-1,6-naphthyridine subtypes, including 5-chloro (subtype 15), 5-aryl (subtype 16), and 5-amino (subtype 17) variants. Analogs were studied for the inhibition of pUL89-C in a biochemical endonuclease assay, a biophysical thermal shift assay (TSA), in silico molecular docking, and for the antiviral potential against HCMV in cell-based assays. These studies identified eight analogs of 8-hydroxy-1,6-naphthyridine-7-carboxamide subtypes for further characterization, most of which inhibited pUL89-C with single-digit μM IC50 values, and conferred antiviral activity in μM range. TSA and molecular modeling of selected analogs corroborate their binding to pUL89-C. Collectively, our biochemical, antiviral, biophysical and in silico data suggest that 8-hydroxy-1,6-naphthyridine-7-carboxamide subtypes can be used for designing inhibitors of HCMV pUL89-C.
Collapse
Affiliation(s)
- Eunkyung Jung
- University of Minnesota College of Pharmacy, Center for Drug Design, UNITED STATES
| | - Ryuichi Majima
- University of Minnesota College of Pharmacy, Center for Drug Design, UNITED STATES
| | - Tiffany C Edwards
- University of Minnesota College of Pharmacy, Center for Drug Design, UNITED STATES
| | - Ruben Soto-Acosta
- University of Minnesota College of Pharmacy, Center for Drug Design, UNITED STATES
| | - Robert J Geraghty
- University of Minnesota College of Pharmacy, Center for Drug Design, UNITED STATES
| | - Zhengqiang Wang
- University of Minnesota Twin Cities, Center for Drug Design, 516 Delaware St Se, 55455, Minneapolis, UNITED STATES
| |
Collapse
|
10
|
Zhang L, Wei F, Borrego D, Zhao F, Río JMD, Frutos-Beltrán E, Zhang J, Xu S, López-Carrobles N, Gao S, Kang D, Pannecouque C, Clercq ED, Liu X, Menéndez-Arias L, Zhan P. Design, synthesis, and biological evaluation of novel double-winged galloyl derivatives as HIV-1 RNase H inhibitors. Eur J Med Chem 2022; 240:114563. [DOI: 10.1016/j.ejmech.2022.114563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 01/18/2023]
|
11
|
He T, Edwards TC, Xie J, Aihara H, Geraghty RJ, Wang Z. 4,5-Dihydroxypyrimidine Methyl Carboxylates, Carboxylic Acids, and Carboxamides as Inhibitors of Human Cytomegalovirus pUL89 Endonuclease. J Med Chem 2022; 65:5830-5849. [PMID: 35377638 PMCID: PMC9441020 DOI: 10.1021/acs.jmedchem.2c00203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human cytomegalovirus (HCMV) terminase complex entails a metal-dependent endonuclease at the C-terminus of pUL89 (pUL89-C). We report herein the design, synthesis, and characterization of dihydroxypyrimidine (DHP) acid (14), methyl ester (13), and amide (15) subtypes as inhibitors of HCMV pUL89-C. All analogs synthesized were tested in an endonuclease assay and a thermal shift assay (TSA) and subjected to molecular docking to predict binding affinity. Although analogs inhibiting pUL89-C in the sub-μM range were identified from all three subtypes, acids (14) showed better overall potency, substantially larger thermal shift, and considerably better docking scores than esters (13) and amides (15). In the cell-based antiviral assay, six analogs inhibited HCMV with moderate activities (EC50 = 14.4-22.8 μM). The acid subtype (14) showed good in vitro ADME properties, except for poor permeability. Overall, our data support the DHP acid subtype (14) as a valuable scaffold for developing antivirals targeting HCMV pUL89-C.
Collapse
Affiliation(s)
- Tianyu He
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Tiffany C Edwards
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jiashu Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Robert J Geraghty
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
12
|
Gao C, Si X, Chi L, Wang H, Dai H, Liu L, Wang Z, Zhang Y, Wang T, Zhou Y, Zheng J, Ke Y, Liu H, Zhang Q. Synthesis and Antiproliferative Activity of 2,4,5,6-Tetrasubstituted Pyrimidine Derivatives Containing Anisole. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202201048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Al-Ghorbani M, Gouda MA, Baashen M, Ranganatha V. L. Pyrimidine-Piperazine Hybrids; Recent Synthesis and Biological Activities. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1998144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Mohammed Al-Ghorbani
- Department of Chemistry, Faculty of Science and Arts, Ulla, Taibah University, Medina, Saudi Arabia
- Department of Chemistry, Faculty of Education, Thamar University, Thamar, Yemen
| | - Moustafa A. Gouda
- Department of Chemistry, Faculty of Science and Arts, Ulla, Taibah University, Medina, Saudi Arabia
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Mohammed Baashen
- Department of Chemistry, Science and Humanities College, Shaqra University, Shaqraa, Saudi Arabia
| | - Lakshmi Ranganatha V.
- Department of Chemistry, The National Institute of Engineering, Mysore, Karnataka, India
| |
Collapse
|
15
|
Metal binding 6-arylthio-3-hydroxypyrimidine-2,4-diones inhibited human cytomegalovirus by targeting the pUL89 endonuclease of the terminase complex. Eur J Med Chem 2021; 222:113640. [PMID: 34147908 DOI: 10.1016/j.ejmech.2021.113640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/18/2022]
Abstract
The genome packaging of human cytomegalovirus (HCMV) requires a divalent metal-dependent endonuclease activity localized to the C-terminus of pUL89 (pUL89-C), which is reminiscent of RNase H-like enzymes in active site structure and catalytic mechanism. Our previous work has shown that metal-binding small molecules can effectively inhibit pUL89-C while conferring significant antiviral activities. In this report we generated a collection of 43 metal-binding small molecules by repurposing analogs of the 6-arylthio-3-hydroxypyrimidine-2,4-dione chemotype previously synthesized for targeting HIV-1 RNase H, and by chemically synthesizing new N-1 analogs. The analogs were subjected to two parallel screening assays: the pUL89-C biochemical assay and the HCMV antiviral assay. Compounds with significant inhibition from each assay were further tested in a dose-response fashion. Single dose cell viability and PAMPA cell permeability were also conducted and considered in selecting compounds for the dose-response antiviral testing. These assays identified a few analogs displaying low μM inhibition against pUL89-C in the biochemical assay and HCMV replication in the antiviral assay. The target engagement was further evaluated via a thermal shift assay using recombinant pUL89-C and molecular docking. Overall, our current work identified novel inhibitors of pUL89-C with significant antiviral activities and further supports targeting pUL89-C with metal-binding small molecules as an antiviral approach against HCMV.
Collapse
|
16
|
Recent Applications of Heteropolyacids and Related Compounds in Heterocycle Synthesis. Contributions between 2010 and 2020. Catalysts 2021. [DOI: 10.3390/catal11020291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Over the past two decades, polyoxometalates (POM) have received considerable attention as solid catalysts, due to their unique physicochemical characteristics, since, first, they have very strong Bronsted acidity, approaching the region of a superacid, and second, they are efficient oxidizers that exhibit rapid redox transformations under fairly mild conditions. Their structural mobility is also highlighted, since they are complex molecules that can be modified by changing their structure or the elements that compose them to model their size, charge density, redox potentials, acidity, and solubility. Finally, they can be used in substoichiometric amounts and reused without an appreciable loss of catalytic activity, all of which postulate them as versatile, economic and ecological catalysts. Therefore, in 2009, we wrote a review article highlighting the great variety of organic reactions, mainly in the area of the synthesis of bioactive heterocycles in which they can be used, and this new review completes that article with the contributions made in the same area for the period 2010 to 2020. The synthesized heterocycles to be covered include pyrimidines, pyridines, pyrroles, indoles, chromenes, xanthenes, pyrans, azlactones, azoles, diazines, azepines, flavones, and formylchromones, among others.
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
He ZX, Zhao TQ, Gong YP, Zhang X, Ma LY, Liu HM. Pyrimidine: A promising scaffold for optimization to develop the inhibitors of ABC transporters. Eur J Med Chem 2020; 200:112458. [PMID: 32497962 DOI: 10.1016/j.ejmech.2020.112458] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/30/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
The multidrug resistance (MDR) phenomenon in cancer cells is the major obstacle leading to failure of chemotherapy accompanied by the feature of intractable and recurrence of cancers. As significant contributors that cause MDR, ABC superfamily proteins can transport the chemotherapeutic drugs out of the tumor cells by the energy of adenosine triphosphate (ATP) hydrolysis, thereby reducing their intracellular accumulation. The ABC transports like ABCB1, ABCC1 and ABCG2 have been extensively studied to develop modulators for overcoming MDR. To date, no reversal agents have been successfully marketed for clinical application, and little information about the ABC proteins bound to specific inhibitors is known, which make the design of MDR inhibitors with potency, selectivity and low toxicity a major challenge. In recent years, it has been increasingly recognized that pyrimidine-based derivatives have the potential for reversing ABC-mediated MDR. In this review, we summarized the pyrimidine-based inhibitors of ABC transporters, and mainly focused on their structure optimizations, development strategies and structure-activity relationship studies in hope of providing a reference for medicinal chemists to develop new modulators of MDR with highly potency and fewer side effects.
Collapse
Affiliation(s)
- Zhang-Xu He
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Tao-Qian Zhao
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Yun-Peng Gong
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Xin Zhang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Li-Ying Ma
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Hong-Min Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, PR China.
| |
Collapse
|
19
|
Corona A, Onnis V, Del Vecchio C, Esposito F, Cheng YC, Tramontano E. 2-(Arylamino)-6-(trifluoromethyl)nicotinic Acid Derivatives: New HIV-1 RT Dual Inhibitors Active on Viral Replication. Molecules 2020; 25:E1338. [PMID: 32183488 PMCID: PMC7144554 DOI: 10.3390/molecules25061338] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/27/2022] Open
Abstract
The persistence of the AIDS epidemic, and the life-long treatment required, indicate the constant need of novel HIV-1 inhibitors. In this scenario the HIV-1 Reverse Transcriptase (RT)-associated ribonuclease H (RNase H) function is a promising drug target. Here we report a series of compounds, developed on the 2-amino-6-(trifluoromethyl)nicotinic acid scaffold, studied as promising RNase H dual inhibitors. Among the 44 tested compounds, 34 inhibited HIV-1 RT-associated RNase H function in the low micromolar range, and seven of them showed also to inhibit viral replication in cell-based assays with a selectivity index up to 10. The most promising compound, 21, inhibited RNase H function with an IC50 of 14 µM and HIV-1 replication in cell-based assays with a selectivity index greater than 10. Mode of action studies revealed that compound 21 is an allosteric dual-site compound inhibiting both HIV-1 RT functions, blocking the polymerase function also in presence of mutations carried by circulating variants resistant to non-nucleoside inhibitors, and the RNase H function interacting with conserved regions within the RNase H domain. Proving compound 21 as a promising lead for the design of new allosteric RNase H inhibitors active against viral replication with not significant cytotoxic effects.
Collapse
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
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
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.
Collapse
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.
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
Gao P, Wang X, Sun L, Cheng X, Poongavanam V, Kongsted J, Álvarez M, Luczkowiak J, Pannecouque C, De Clercq E, Lee KH, Chen CH, Liu H, Menéndez-Arias L, Liu X, Zhan P. Design, synthesis, and biologic evaluation of novel galloyl derivatives as HIV-1 RNase H inhibitors. Chem Biol Drug Des 2019; 93:582-589. [PMID: 30560566 DOI: 10.1111/cbdd.13455] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/13/2018] [Accepted: 11/24/2018] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated ribonuclease H (RNase H) remains as the only enzyme encoded within the viral genome not targeted by current antiviral drugs. In this work, we report the design, synthesis, and biologic evaluation of a novel series of galloyl derivatives with HIV-1 RNase H inhibitory activity. Most of them showed IC50 s at sub- to low-micromolar concentrations in enzymatic assays. The most potent compound was II-25 that showed an IC50 of 0.72 ± 0.07 μM in RNase H inhibition assays carried out with the HIV-1BH 10 RT. II-25 was 2.8 times more potent than β-thujaplicinol in these assays. Interestingly, II-25 and other galloyl derivatives were also found to inhibit the HIV IN strand transfer activity in vitro. Structure-activity relationships (SAR) studies and molecular modeling analysis predict key interactions with RT residues His539 and Arg557, while providing helpful insight for further optimization of selected compounds.
Collapse
Affiliation(s)
- Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, China
| | - Xueshun Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, China
| | - Xiqiang Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, China
| | | | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Mar Álvarez
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Madrid, Spain
| | - Joanna Luczkowiak
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Madrid, Spain
| | | | - Erik De Clercq
- Rega Institute for Medical Research, K.U.Leuven, Leuven, Belgium
| | - Kuo-Hsiung Lee
- Natural Products Research Laboratories, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina
| | - Chin-Ho Chen
- Surgical Science, Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Huiqing Liu
- Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Madrid, Spain
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan, China
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|