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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.
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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.)
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Sun Q, Biswas A, Lyumkis D, Levy R, Deng N. Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization. Viruses 2024; 16:76. [PMID: 38257776 PMCID: PMC11154245 DOI: 10.3390/v16010076] [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: 11/25/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
The first- and second-generation clinically used HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) are key components of antiretroviral therapy (ART), which work by blocking the integration step in the HIV-1 replication cycle that is catalyzed by a nucleoprotein assembly called an intasome. However, resistance to even the latest clinically used INSTIs is beginning to emerge. Developmental third-generation INSTIs, based on naphthyridine scaffolds, are promising candidates to combat drug-resistant viral variants. Among these novel INSTIs, compound 4f exhibits two distinct conformations when binding with intasomes from HIV-1 and the closely related prototype foamy virus (PFV) despite the high structural similarity of their INSTI binding pockets. The molecular mechanism and the key active site residues responsible for these differing binding modes in closely related intasomes remain elusive. To unravel the molecular determinants governing the two distinct binding modes, we applied a novel molecular dynamics-based free energy method that utilizes alchemical pathways to overcome the sampling challenges associated with transitioning between the two bound conformations of ligand 4f within the crowded environments of the INSTI binding pockets in these intasomes. The calculated conformational free energies successfully recapitulate the experimentally observed binding mode preferences in the two viral intasomes. Analysis of the simulated structures suggests that the observed binding mode preferences are caused by amino acid residue differences in both the front and the central catalytic sub-pocket of the INSTI binding site in HIV-1 and PFV. Additional free energy calculations on mutants of HIV-1 and PFV revealed that while both sub-pockets contribute to binding mode selection, the central sub-pocket plays a more important role. These results highlight the importance of both side chain and solvent reorganization, as well as the conformational entropy in determining the ligand binding mode, and will help inform the development of more effective INSTIs for combatting drug-resistant viral variants.
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Affiliation(s)
- Qinfang Sun
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA; (Q.S.); (R.L.)
| | - Avik Biswas
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (A.B.); (D.L.)
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (A.B.); (D.L.)
- Graduate Schools for Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Ronald Levy
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA; (Q.S.); (R.L.)
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, NY 10038, USA
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Sun Q, Biswas A, Lyumkis D, Levy R, Deng N. Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569269. [PMID: 38077045 PMCID: PMC10705364 DOI: 10.1101/2023.11.29.569269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
The first and second-generation clinically used HIV-1 integrase (IN) strand transfer inhibitors (INSTIs) are key components of antiretroviral therapy (ART), which work by blocking the integration step in the HIV-1 replication cycle that is catalyzed by a nucleoprotein assembly called an intasome. However, resistance to even the latest clinically used INSTIs is beginning to emerge. Developmental third-generation INSTIs, based on naphthyridine scaffold, are promising candidates to combat drug-resistant viral variants. Among these novel INSTIs, compound 4f exhibits two distinct conformations when binding to intasomes from HIV-1 and the closely related prototype foamy virus (PFV), despite the high structural similarity of their INSTI binding pockets. The molecular mechanism and the key active site residues responsible for these differing binding modes in closely related intasomes remain elusive. To unravel the molecular determinants governing the two distinct binding modes, we employ a novel molecular dynamics-based free energy approach that utilizes alchemical pathways to overcome the sampling challenges associated with transitioning between two ligand conformations within crowded environments along physical pathways. The calculated conformational free energies successfully recapitulate the experimentally observed binding mode preferences in the two viral intasomes. Analysis of the simulated structures suggests that the observed binding mode preferences are caused by amino acid residue differences in both the front and the central catalytic sub-pocket of the INSTI binding site in HIV-1 and PFV. Additional free energy calculations on mutants of HIV-1 and PFV revealed that while both sub-pockets contribute to the binding mode selection, the central sub-pocket plays a more important role. These results highlight the importance of both side chain and solvent reorganization, as well as the conformational entropy in determining the ligand binding mode and will help inform the development of more effective INSTIs for combatting drug-resistant viral variants.
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Affiliation(s)
- Qinfang Sun
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA 19122
| | - Avik Biswas
- The Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, CA 92037
- Department of Physics, University of California San Diego, La Jolla, CA, 92093
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, Laboratory of Genetics, La Jolla, CA 92037
- Graduate schools for Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA, 92093
| | - Ronald Levy
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA 19122
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, NY10038
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Echefu SN, Udosen JE, Akwiwu EC, Akpotuzor JO, Obeagu EI. Effect of Dolutegravir regimen against other regimens on some hematological parameters, CD4 count and viral load of people living with HIV infection in South Eastern Nigeria. Medicine (Baltimore) 2023; 102:e35910. [PMID: 38013350 PMCID: PMC10681510 DOI: 10.1097/md.0000000000035910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/28/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Appropriate usage of highly active antiretroviral therapy (HAART) suppresses human immunodeficiency virus (HIV) replication. One of such HAART is dolutegravir (DTG) containing regimen which Nigeria included in her national protocol, as the preferred first-line option, with particularly fixed dose combination of tenofovir/lamivudine/dolutegravir (TLD) in 2018. AIM To access the impact of this regimen as against other regimens on some hematological parameters as well as cluster of differentiation 4 (CD4) count and viral load on people living with HIV infection. METHODS The study site is a health facility center supported by President Emergency Plan for acquired immunodeficiency syndrome (AIDS) Relief where people living with HIV infection (PLWHIV) visit for their routine management in Abakaliki, Ebonyi State. A hundred and twenty-two (122) subjects participated, 58 PLWHIV and 64 control subjects. CD4 + count by partec cyflow auto analyzer, while the Viral load assay was by Roche COBAS Ampriplep/COBAS TaqMan molecular systems. Full blood count determination was by Sysmex XE-2100 hematology auto analyzer, while the detection of antibody to HAART was by Petz and direct Coombs tests. RESULTS Mean values of hemoglobin (Hb), Total white cell count, Lymphocytes, Monocytes and CD4 + counts of people living with HIV infection (PLWHIV) were significantly (P = .0001) lower than the control subjects. The Hb level of PLWHIV on Efavirenz combination (TDF/3TC/EFV) are comparable 123 ± 32g/l with those on Ritonavir combination (TDF/3TC/LPV/R) 136 ± 16g/l and Dolutegravir (TLD)134 ± 20.0g/l (P = .307). On the other hand, total white cell count (4.55 ± 1.99 × 109/L) of those on Efavirenz combination (TDF/3TC/EFV) and Dolutegravir (TLD) (4.53 ± 1.31 × 109/L) were significantly higher than those on Ritonavir combination (TDF/3TC/LPV/R) (4.09 ± 1.15 × 109/L). The Viral Load of PLWHIV on Dolutegravir (TLD) was significantly lower 171.57 ± 4.56 copies/mL than those on Efavirenz combination (TDF/3TC/EFV) (86,395.91 ± 27,476.57copies/mL) and Ritonavir combination (TDF/3TC/LPV/R) (81,188.83 ± 13,393.47 copies/mL), respectively. CONCLUSION Some hematological parameters (such as Hb, total white cell counts and CD4 + count) were lower in people living with HIV than values seen in control group. The 3 regimens used in the management of HIV infection in the locality revealed comparable Packed cell volume and Hemoglobin levels. Total white cell count of those on Efavirenz and DTG is comparable with higher values than those on Ritonavir.
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Affiliation(s)
- Stella N. Echefu
- Alex Ekwume Federal University Teaching Hospital Abakaliki, Ebonyi State, Nigeria
| | | | - Euphoria C. Akwiwu
- Department of Haematology and Blood Transfusion Science, University of Calabar, Nigeria
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Renzi G, Carta F, Supuran CT. The Integrase: An Overview of a Key Player Enzyme in the Antiviral Scenario. Int J Mol Sci 2023; 24:12187. [PMID: 37569561 PMCID: PMC10419282 DOI: 10.3390/ijms241512187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Integration of a desossiribonucleic acid (DNA) copy of the viral ribonucleic acid (RNA) into host genomes is a fundamental step in the replication cycle of all retroviruses. The highly conserved virus-encoded Integrase enzyme (IN; EC 2.7.7.49) catalyzes such a process by means of two consecutive reactions named 3'-processing (3-P) and strand transfer (ST). The Authors report and discuss the major discoveries and advances which mainly contributed to the development of Human Immunodeficiency Virus (HIV) -IN targeted inhibitors for therapeutic applications. All the knowledge accumulated over the years continues to serve as a valuable resource for the design and development of effective antiretroviral drugs.
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Affiliation(s)
| | - Fabrizio Carta
- Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA) Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, Via Ugo Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (G.R.); (C.T.S.)
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Taoda Y, Sugiyama S, Seki T. New designs for HIV-1 integrase inhibitors: a patent review (2018-present). Expert Opin Ther Pat 2023; 33:51-66. [PMID: 36750766 DOI: 10.1080/13543776.2023.2178300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
INTRODUCTION Combination antiretroviral therapy (cART) has dramatically reduced morbidity and mortality of HIV-1-infected patients. Integrase strand transfer inhibitors (INSTIs) play an important role as a key drug in cART. The second-generation INSTIs are very potent, but due to the emergence of highly resistant viruses and the demand for more conveniently usable drugs, the development of 'third-generation' INSTIs and mechanistically different inhibitors is actively being pursued. AREAS COVERED This article reviews the patents (from 2018 to the present) for two classes of HIV-1 integrase inhibitors of INSTIs and integrase-LEDGF/p75 allosteric inhibitors (INLAIs). EXPERT OPINION Since the approval of the second-generation INSTI dolutegravir, the design of new INSTIs has been mostly focused on its scaffold, carbamoylpyridone (CAP). This CAP scaffold is used not only for HIV-1 INSTIs but also for drug discoveries targeting other viral enzymes. With the approval of cabotegravir as a regimen of long-acting injection in combination with rilpivirine, there is a growing need for longer-acting agents. INLAIs have been intensely studied by many groups but have yet to reach the market. However, INLAIs have recently been reported to also function as a latency promoting agent (LPA), indicating further development possibilities.
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Affiliation(s)
- Yoshiyuki Taoda
- Laboratory for Medicinal Chemistry Research, Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd, Toyonaka-shi, Japan
| | - Shuichi Sugiyama
- Laboratory for Medicinal Chemistry Research, Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd, Toyonaka-shi, Japan
| | - Takahiro Seki
- Laboratory for Medicinal Chemistry Research, Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd, Toyonaka-shi, Japan
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Abdollahi O, Mahboubi A, Hajimahdi Z, Zarghi A. Design, Synthesis, Docking Study, and Biological Evaluation of 4-hydroxy-2-oxo-1,2-dihydroquinoline-3-carbohydrazide Derivatives as Anti-HIV-1 and Antibacterial Agents. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH 2022; 21:e126562. [PMID: 36060913 PMCID: PMC9420229 DOI: 10.5812/ijpr-126562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/22/2021] [Accepted: 03/07/2022] [Indexed: 11/16/2022]
Abstract
Background: The emergence of drug resistance to the existing antibacterial and anti-HIV-1 therapeutics has posed an urgent medical need to develop new molecules. We describe in this regard, a series of novel N'-arylidene-4-hydroxy-2-oxo-1,2-dihydroquinoline-3-carbohydrazide derivatives with anti-HIV-1 and antibacterial activities were designed and synthesized in this study. Methods: The synthesized compounds were evaluated for the blocking of both the IN ST process and cell-based HIV-1 replication. The synthesized compounds were also examined for in vitro antibacterial activities using the minimum inhibitory concentration (MIC) assay. Results: The results revealed the moderate antibacterial activity of the synthesized compounds. Moreover, no significant integrase inhibitory and anti-HIV-1 activities were observed for the synthesized compounds at concentrations < 100 µM. Conclusions: According to the docking analyses, the orientation of the designed scaffold in the active site of integrase is similar to the other inhibitors of the HIV integrase and can be regarded as an acceptable template for further structural modification to improve potencies.
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Affiliation(s)
- Omid Abdollahi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arash Mahboubi
- Department of Pharmaceutics and Pharmaceutical Nanotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Hajimahdi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afshin Zarghi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Corresponding Author: Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran. Tel: +98-218820096, Fax: +98-2188665341,
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Abstract
The majority of drug discovery efforts against herpesviruses have focused on nucleoside analogs that target viral DNA polymerases, agents that are associated with dose-limiting toxicity and/or a narrow spectrum of activity. We are pursuing a strategy based on targeting two-metal ion-dependent (TMID) viral enzymes. This family of enzymes consists of structurally related proteins that share common active sites containing conserved carboxylates predicted to coordinate divalent cations essential for catalysis. Compounds that target TMID enzymes, such as HIV integrase and influenza endoribonuclease, have been successfully developed for clinical use. HIV integrase inhibitors have been reported to inhibit replication of herpes simplex virus (HSV) and other herpesviruses; however, the molecular targets of their antiviral activities have not been identified. We employed a candidate-based approach utilizing several two-metal-directed chemotypes and the potential viral TMID enzymatic targets in an effort to correlate target-based activity with antiviral potency. The panel of compounds tested included integrase inhibitors, the anti-influenza agent baloxavir, three natural products previously shown to exhibit anti-HSV activity, and two 8-hydroxyquinolines (8-HQs), AK-157 and AK-166, from our in-house program. The integrase inhibitors exhibited weak overall anti-HSV-1 activity, while the 8-HQs were shown to inhibit both HSV-1 and cytomegalovirus (CMV). Target-based analysis demonstrated that none of the antiviral compounds acted by inhibiting ICP8, contradicting previous reports. On the other hand, baloxavir inhibited the proofreading exonuclease of HSV polymerase, while AK-157 and AK-166 inhibited the alkaline exonuclease UL12. In addition, AK-157 also inhibited the catalytic activity of the HSV polymerase, which provides an opportunity to potentially develop dual-targeting agents against herpesviruses. IMPORTANCE Human herpesviruses (HHVs) establish lifelong latent infections, which undergo periodic reactivation and remain a major cause of morbidity and mortality, especially in immunocompromised individuals. Currently, HHV infections are treated primarily with agents that target viral DNA polymerase, including nucleoside analogs; however, long-term treatment can be complicated by the development of drug resistance. New therapies with novel modes of action would be important not only for the treatment of resistant viruses but also for use in combination therapy to reduce dose-limiting toxicities and potentially eliminate infection. Since many essential HHV proteins are well conserved, inhibitors of novel targets would ideally exhibit broad-spectrum activity against multiple HHVs.
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N-4 Alkyl Cytosine Derivatives Synthesis: A New Approach. REACTIONS 2022. [DOI: 10.3390/reactions3010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The selective N-4 alkylation of cytosine plays a critical role in the synthesis of biologically active molecules. This work focuses on the development of practical reaction conditions toward a regioselective synthesis of N-4-alkyl cytosine derivatives. The sequence includes a direct and selective sulfonylation at the N-1 site of the cytosine, followed by the alkylation of the amino site using KHMDS in CH2Cl2/THF mixture, providing a fast and efficient approach consistent with pyrimidine-based drug design.
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Chen Q, Wu C, Zhu J, Li E, Xu Z. Therapeutic potential of indole derivatives as anti-HIV agents: A mini-review. Curr Top Med Chem 2021; 22:993-1008. [PMID: 34636313 DOI: 10.2174/1568026621666211012111901] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 11/22/2022]
Abstract
Acquired immunodeficiency syndrome (AIDS), caused by human immunodeficiency virus (HIV), is one of the leading causes of human deaths. The advent of different anti-HIV drugs over different disease progress has made AIDS/HIV from a deadly infection to chronic and manageable disease. However, the development of multidrug-resistant viruses, together with the severe side effects of anti-HIV agents, compromised their efficacy and limited the treatment options. Indoles, the most common frameworks in the bioactive molecules, represent attractive scaffolds for the design and development of novel drugs. Indole derivatives are potential inhibitors of HIV enzymes such as reverse transcriptase, integrase and protease, and some indole-based agents like Delavirdine have already been applied in clinics or under clinical evaluations for the treatment of AIDS/HIV, revealing that indole moiety is a useful template for the development of anti-HIV agents. This review focuses on the recent advancement of indole derivatives including indole alkaloids, hybrids, and dimers with anti-HIV potential, covering articles published between 2010 and 2020. The chemical structures, structure-activity relationship and mechanisms of action are also discussed.
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Affiliation(s)
- Qingtai Chen
- School of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian, 463000. China
| | - Chongchong Wu
- Department of Chemical and Petroleum Engineering, University of Calgary, T2N 1N4 Calgary, Alberta. Canada
| | - Jinjin Zhu
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian, 463000. China
| | - Enzhong Li
- School of Biological and Food Processing Engineering, Huanghuai University, Zhumadian, 463000. China
| | - Zhi Xu
- School of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian, 463000. China
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Identification of Potential Drug Targets of Broad-Spectrum Inhibitors with a Michael Acceptor Moiety Using Shotgun Proteomics. Viruses 2021; 13:v13091756. [PMID: 34578337 PMCID: PMC8473112 DOI: 10.3390/v13091756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 01/10/2023] Open
Abstract
The Michael addition reaction is a spontaneous and quick chemical reaction that is widely applied in various fields. This reaction is performed by conjugating an addition of nucleophiles with α, β-unsaturated carbonyl compounds, resulting in the bond formation of C-N, C-S, C-O, and so on. In the development of molecular materials, the Michael addition is not only used to synthesize chemical compounds but is also involved in the mechanism of drug action. Several covalent drugs that bond via Michael addition are regarded as anticarcinogens and anti-inflammatory drugs. Although drug development is mainly focused on pharmaceutical drug discovery, target-based discovery can provide a different perspective for drug usage. However, considerable time and labor are required to define a molecular target through molecular biological experiments. In this review, we systematically examine the chemical structures of current FDA-approved antiviral drugs for potential Michael addition moieties with α, β-unsaturated carbonyl groups, which may exert an unidentified broad-spectrum inhibitory mechanism to target viral or host factors. We thus propose that profiling the targets of antiviral agents, such as Michael addition products, can be achieved by employing a high-throughput LC-MS approach to comprehensively analyze the interaction between drugs and targets, and the subsequent drug responses in the cellular environment to facilitate drug repurposing and/or identify potential adverse effects, with a particular emphasis on the pros and cons of this shotgun proteomic approach.
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Fata F, Silvestri I, Ardini M, Ippoliti R, Di Leandro L, Demitri N, Polentarutti M, Di Matteo A, Lyu H, Thatcher GR, Petukhov PA, Williams DL, Angelucci F. Probing the Surface of a Parasite Drug Target Thioredoxin Glutathione Reductase Using Small Molecule Fragments. ACS Infect Dis 2021; 7:1932-1944. [PMID: 33950676 DOI: 10.1021/acsinfecdis.0c00909] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fragment screening is a powerful drug discovery approach particularly useful for enzymes difficult to inhibit selectively, such as the thiol/selenol-dependent thioredoxin reductases (TrxRs), which are essential and druggable in several infectious diseases. Several known inhibitors are reactive electrophiles targeting the selenocysteine-containing C-terminus and thus often suffering from off-target reactivity in vivo. The lack of structural information on the interaction modalities of the C-terminus-targeting inhibitors, due to the high mobility of this domain and the lack of alternative druggable sites, prevents the development of selective inhibitors for TrxRs. In this work, fragments selected from actives identified in a large screen carried out against Thioredoxin Glutathione Reductase from Schistosoma mansoni (SmTGR) were probed by X-ray crystallography. SmTGR is one of the most promising drug targets for schistosomiasis, a devastating, neglected disease. Utilizing a multicrystal method to analyze electron density maps, structural analysis, and functional studies, three binding sites were characterized in SmTGR: two sites are close to or partially superposable with the NADPH binding site, while the third one is found between two symmetry related SmTGR subunits of the crystal lattice. Surprisingly, one compound bound to this latter site stabilizes, through allosteric effects mediated by the so-called guiding bar residues, the crucial redox active C-terminus of SmTGR, making it finally visible at high resolution. These results further promote fragments as small molecule probes for investigating functional aspects of the target protein, exemplified by the allosteric effect on the C-terminus, and providing fundamental chemical information exploitable in drug discovery.
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Affiliation(s)
- Francesca Fata
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Ilaria Silvestri
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Matteo Ardini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Rodolfo Ippoliti
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Luana Di Leandro
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Nicola Demitri
- Elettra − Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, 34149 Basovizza − Trieste, Italy
| | - Maurizio Polentarutti
- Elettra − Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, 34149 Basovizza − Trieste, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology, National Research Council of Italy, c/o Department of Biochemical Sciences “A Rossi Fanelli” - Sapienza University of Rome, 00185 Rome, Italy
| | - Haining Lyu
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Gregory R.J. Thatcher
- Department of Pharmacology & Toxicology, College of Pharmacy, the University of Arizona, Tucson, Arizona 85721, United States
| | - Pavel A. Petukhov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - David L. Williams
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Francesco Angelucci
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
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13
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Panwar U, Singh SK. In silico virtual screening of potent inhibitor to hamper the interaction between HIV-1 integrase and LEDGF/p75 interaction using E-pharmacophore modeling, molecular docking, and dynamics simulations. Comput Biol Chem 2021; 93:107509. [PMID: 34153658 DOI: 10.1016/j.compbiolchem.2021.107509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023]
Abstract
The rapid increase of HIV-1 infection throughout the globe has a high demand for a superior drug with lesser side effects. LEDGF/p75, the human Lens Epithelium-Derived Growth Factor is identified as a promising cellular cofactor with integrase in facilitating the viral replication in an early stage by acting as a tethering factor in the pre-integration to the chromatin. Therefore, the present study was designed to identify a potent inhibitor by applying an E-pharmacophore based virtual screening, molecular docking, and dynamics simulation approaches. Finally, ZINC22077550 and ZINC32124441 were best identified potent molecules with the efficient binding affinity, strong hydrogen bonding, and acceptable pharmacological properties to hamper the interaction between integrase and LEDGF/p75. Further, the DFT and MDS studies were also analyzed, and shown a favorable energetic state and dynamic stability then reference compound. In conclusion, we suggest that these findings could be novel therapeutics in the future and may increase the lifespan of individuals suffering from viral infection.
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Affiliation(s)
- Umesh Panwar
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India.
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14
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Messore A, Corona A, Madia VN, Saccoliti F, Tudino V, De Leo A, Ialongo D, Scipione L, De Vita D, Amendola G, Novellino E, Cosconati S, Métifiot M, Andreola ML, Esposito F, Grandi N, Tramontano E, Costi R, Di Santo R. Quinolinonyl Non-Diketo Acid Derivatives as Inhibitors of HIV-1 Ribonuclease H and Polymerase Functions of Reverse Transcriptase. J Med Chem 2021; 64:8579-8598. [PMID: 34106711 PMCID: PMC8279492 DOI: 10.1021/acs.jmedchem.1c00535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Novel anti-HIV agents
are still needed to overcome resistance issues,
in particular inhibitors acting against novel viral targets. The ribonuclease
H (RNase H) function of the reverse transcriptase (RT) represents
a validated and promising target, and no inhibitor has reached the
clinical pipeline yet. Here, we present rationally designed non-diketo
acid selective RNase H inhibitors (RHIs) based on the quinolinone
scaffold starting from former dual integrase (IN)/RNase H quinolinonyl
diketo acids. Several derivatives were synthesized and tested against
RNase H and viral replication and found active at micromolar concentrations.
Docking studies within the RNase H catalytic site, coupled with site-directed
mutagenesis, and Mg2+ titration experiments demonstrated
that our compounds coordinate the Mg2+ cofactor and interact
with amino acids of the RNase H domain that are highly conserved among
naïve and treatment-experienced patients. In general, the new
inhibitors influenced also the polymerase activity of RT but were
selective against RNase H vs the IN enzyme.
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Affiliation(s)
- Antonella Messore
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Valentina Noemi Madia
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Francesco Saccoliti
- D3 PharmaChemistry, Italian Institute of Technology, Via Morego 30, I-16163 Genova, Italy
| | - Valeria Tudino
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Alessandro De Leo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Davide Ialongo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Luigi Scipione
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Daniela De Vita
- Department of Environmental Biology, "Sapienza" University of Rome, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Giorgio Amendola
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Ettore Novellino
- Department of Pharmacy, University Federico II of Naples, Via D. Montesano 49, 80131 Naples, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Mathieu Métifiot
- Laboratoire MFP, UMR 5234, CNRS - Université de Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux cedex, France
| | - Marie-Line Andreola
- Laboratoire MFP, UMR 5234, CNRS - Université de Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux cedex, France
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554-09042 Monserrato (CA), Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, p.le Aldo Moro 5, I-00185 Rome, Italy
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Vanangamudi M, Kurup S, Namasivayam V. Non-nucleoside reverse transcriptase inhibitors (NNRTIs): a brief overview of clinically approved drugs and combination regimens. Curr Opin Pharmacol 2020; 54:179-187. [PMID: 33202360 DOI: 10.1016/j.coph.2020.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 12/27/2022]
Abstract
The non-nucleoside reverse transcriptase inhibitors (NNRTIs) are allosteric inhibitors of HIV-1 reverse transcriptase and are classified into generations depending on their discovery and resistance profiles. The NNRTIs are used in combination regimens with antiretroviral agents that target two or more enzymes in the viral life cycle. The combination regimens usually include a backbone of two nucleoside or nucleotide reverse transcriptase inhibitors and a third core agent among the NNRTIs or protease inhibitors. The combination regimens are maintained over long durations and consequently lead to long-term problems, including toxicity, drug-drug interactions, and increasing costs. This brief overview summarizes the pharmacokinetic profiles for NNRTIs and NNRTI-based combination regimens.
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Affiliation(s)
- Murugesan Vanangamudi
- Department of Medicinal and Pharmaceutical Chemistry, Sree Vidyanikethan College of Pharmacy, Tirupathi, Andhra Pradesh 517102, India
| | - Sonali Kurup
- College of Pharmacy, Ferris State University, 220 Ferris Drive, Big Rapids, MI 49301, USA
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16
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Molecular dynamic simulations to investigate the structural impact of known drug resistance mutations on HIV-1C Integrase-Dolutegravir binding. PLoS One 2020; 15:e0223464. [PMID: 32379830 PMCID: PMC7205217 DOI: 10.1371/journal.pone.0223464] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/21/2020] [Indexed: 12/18/2022] Open
Abstract
Resistance associated mutations (RAMs) threaten the long-term success of combination antiretroviral therapy (cART) outcomes for HIV-1 treatment. HIV-1 Integrase (IN) strand transfer inhibitors (INSTIs) have proven to be a viable option for highly specific HIV-1 therapy. The INSTI, Dolutegravir is recommended by the World Health Organization for use as first-line cART. This study aims to understand how RAMs affect the stability of IN, as well as the binding of the drug Dolutegravir to the catalytic pocket of the protein. A homology model of HIV-1 subtype C IN was successfully constructed and validated. The site directed mutator webserver was used to predict destabilizing and/or stabilizing effects of known RAMs while FoldX confirmed any changes in protein energy upon introduction of mutation. Also, interaction analysis was performed between neighbouring residues. Three mutations known to be associated with Raltegravir, Elvitegravir and Dolutegravir resistance were selected; E92Q, G140S and Y143R, for molecular dynamics simulations. The structural quality assessment indicated high reliability of the HIV-1C IN tetrameric structure, with more than 90% confidence in modelled regions. Change in free energy for the three mutants indicated different effects, while simulation analysis showed G140S to have the largest affect on protein stability and flexibility. This was further supported by weaker non-bonded pairwise interaction energy and binding free energy values between the drug DTG and E92Q, Y143R and G140S mutants suggesting reduced binding affinity, as indicated by interaction analysis in comparison to the WT. Our findings suggest the G140S mutant has the strongest effect on the HIV-1C IN protein structure and Dolutegravir binding. To the best of our knowledge, this is the first study that uses the consensus wild type HIV-1C IN sequence to build an accurate 3D model to understand the effect of three known mutations on DTG drug binding in a South Africa context.
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Mușat MG, Nițulescu GM, Surleac M, Tsatsakis A, Spandidos DA, Margină D. HIV‑1 integrase inhibitors targeting various DDE transposases: Retroviral integration versus RAG‑mediated recombination (Review). Mol Med Rep 2019; 20:4749-4762. [PMID: 31702817 PMCID: PMC6854553 DOI: 10.3892/mmr.2019.10777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/25/2019] [Indexed: 12/18/2022] Open
Abstract
Transposases are ubiquitous mobile genetic elements responsible for genome development, driving rearrangements, such as insertions, deletions and translocations. Across species evolution, some transposases are tamed by their host and are made part of complex cellular systems. The proliferation of retroviruses is also dependent on transposase related enzymes termed integrases. Recombination‑activating gene protein (RAG)1 and metnase are just two examples of transposase domestication and together with retroviral integrases (INs), they belong to the DDE polynucleotidyl transferases superfamily. They share mechanistic and structural features linked to the RNase H‑like fold, harboring a DDE(D) metal dependent catalytic motif. Recent antiretroviral compounds target the catalytic domain of integrase, but they also have the potential of inhibiting other related enzymes. In this review, we report the activity of different classes of integrase inhibitors on various DDE transposases. Computational simulations are useful to predict the extent of off‑target activity and have been employed to study the interactions between RAG1 recombinase and compounds from three different pharmacologic classes. We demonstrate that strand‑transfer inhibitors display a higher affinity towards the RAG1 RNase H domain, as suggested by experimental data compared to allosteric inhibitors. While interference with RAG1 and 2 recombination is associated with a negative impact on immune function, the inhibition of metnase or HTLV‑1 integrase opens the way for the development of novel therapies for refractory cancers.
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Affiliation(s)
- Mihaela Georgiana Mușat
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - George Mihai Nițulescu
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Marius Surleac
- National Institute for Infectious Diseases ‘Matei Bals’, 021105 Bucharest, Romania
| | - Aristidis Tsatsakis
- Department of Forensic Sciences and Toxicology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Denisa Margină
- Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020956 Bucharest, Romania
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18
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Sirous H, Chemi G, Gemma S, Butini S, Debyser Z, Christ F, Saghaie L, Brogi S, Fassihi A, Campiani G, Brindisi M. Identification of Novel 3-Hydroxy-pyran-4-One Derivatives as Potent HIV-1 Integrase Inhibitors Using in silico Structure-Based Combinatorial Library Design Approach. Front Chem 2019; 7:574. [PMID: 31457006 PMCID: PMC6700280 DOI: 10.3389/fchem.2019.00574] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 07/29/2019] [Indexed: 11/16/2022] Open
Abstract
We describe herein the development and experimental validation of a computational protocol for optimizing a series of 3-hydroxy-pyran-4-one derivatives as HIV integrase inhibitors (HIV INIs). Starting from a previously developed micromolar inhibitors of HIV integrase (HIV IN), we performed an in-depth investigation based on an in silico structure-based combinatorial library designing approach. This method allowed us to combine a combinatorial library design and side chain hopping with Quantum Polarized Ligand Docking (QPLD) studies and Molecular Dynamics (MD) simulation. The combinatorial library design allowed the identification of the best decorations for our promising scaffold. The resulting compounds were assessed by the mentioned QPLD methodology using a homology model of full-length binary HIV IN/DNA for retrieving the best performing compounds acting as HIV INIs. Along with the prediction of physico-chemical properties, we were able to select a limited number of drug-like compounds potentially displaying potent HIV IN inhibition. From this final set, based on the synthetic accessibility, we further shortlisted three representative compounds for the synthesis. The compounds were experimentally assessed in vitro for evaluating overall HIV-1 IN inhibition, HIV-1 IN strand transfer activity inhibition, HIV-1 activity inhibition and cellular toxicity. Gratifyingly, all of them showed relevant inhibitory activity in the in vitro tests along with no toxicity. Among them HPCAR-28 represents the most promising compound as potential anti-HIV agent, showing inhibitory activity against HIV IN in the low nanomolar range, comparable to that found for Raltegravir, and relevant potency in inhibiting HIV-1 replication and HIV-1 IN strand transfer activity. In summary, our results outline HPCAR-28 as a useful optimized hit for the potential treatment of HIV-1 infection by targeting HIV IN.
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Affiliation(s)
- Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Giulia Chemi
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Siena, Italy
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Siena, Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Siena, Italy
| | - Zeger Debyser
- Molecular Medicine, K.U. Leuven and IRC KULAK, Leuven, Belgium
| | - Frauke Christ
- Molecular Medicine, K.U. Leuven and IRC KULAK, Leuven, Belgium
| | - Lotfollah Saghaie
- Department of Medicinal Chemistry, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Afshin Fassihi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Siena, Italy
| | - Margherita Brindisi
- Department of Pharmacy, Department of Excellence 2018-2022, University of Naples Federico II, Naples, Italy
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19
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Savosina PI, Stolbov LA, Druzhilovskiy DS, Filimonov DA, Nicklaus MC, Poroikov VV. [Discovering new antiretroviral compounds in "Big Data" chemical space of the SAVI library]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2019; 65:73-79. [PMID: 30950810 DOI: 10.18097/pbmc20196502073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Despite significant advances in the application of highly active antiretroviral therapy, the development of new drugs for the treatment of HIV infection remains an important task because the existing drugs do not provide a complete cure, cause serious side effects and lead to the emergence of resistance. In 2015, a consortium of American and European scientists and specialists launched a project to create the SAVI (Synthetically Accessible Virtual Inventory) library. Its 2016 version of over 283 million structures of new easily synthesizable organic molecules, each annotated with a proposed synthetic route, were generated <i>in silico</i> for the purpose of searching for safer and more potent pharmacological substances. We have developed an algorithm for comparing large chemical databases (DB) based on the representation of structural formulas in SMILES codes, and evaluated the possibility of detecting new antiretroviral compounds in the SAVI database. After analyzing the intersection of SAVI with 97 million structures of the PubChem database, we found that only a small part of the SAVI (~0.015%) is represented in PubChem, which indicates a significant novelty of this virtual library. However, among those structures, 632 compounds tested for anti-HIV activity were detected, 41 of which had the desired activity. Thus, our studies for the first time demonstrated that SAVI is a promising source for the search for new anti-HIV compounds.
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Affiliation(s)
- P I Savosina
- Institute of Biomedical Chemistry, Moscow, Russia
| | - L A Stolbov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - M C Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States
| | - V V Poroikov
- Institute of Biomedical Chemistry, Moscow, Russia
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20
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Pinto DO, Scott TA, DeMarino C, Pleet ML, Vo TT, Saifuddin M, Kovalskyy D, Erickson J, Cowen M, Barclay RA, Zeng C, Weinberg MS, Kashanchi F. Effect of transcription inhibition and generation of suppressive viral non-coding RNAs. Retrovirology 2019; 16:13. [PMID: 31036006 PMCID: PMC6489247 DOI: 10.1186/s12977-019-0475-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 04/20/2019] [Indexed: 01/03/2023] Open
Abstract
Background HIV-1 patients receiving combination antiretroviral therapy (cART) survive infection but require life-long adherence at high expense. In chronic cART-treated patients with undetectable viral titers, cell-associated viral RNA is still detectable, pointing to low-level viral transcriptional leakiness. To date, there are no FDA-approved drugs against HIV-1 transcription. We have previously shown that F07#13, a third generation Tat peptide mimetic with competitive activity against Cdk9/T1-Tat binding sites, inhibits HIV-1 transcription in vitro and in vivo. Results Here, we demonstrate that increasing concentrations of F07#13 (0.01, 0.1, 1 µM) cause a decrease in Tat levels in a dose-dependent manner by inhibiting the Cdk9/T1-Tat complex formation and subsequent ubiquitin-mediated Tat sequestration and degradation. Our data indicate that complexes I and IV contain distinct patterns of ubiquitinated Tat and that transcriptional inhibition induced by F07#13 causes an overall reduction in Tat levels. This reduction may be triggered by F07#13 but ultimately is mediated by TAR-gag viral RNAs that bind suppressive transcription factors (similar to 7SK, NRON, HOTAIR, and Xist lncRNAs) to enhance transcriptional gene silencing and latency. These RNAs complex with PRC2, Sin3A, and Cul4B, resulting in epigenetic modifications. Finally, we observed an F07#13-mediated decrease of viral burden by targeting the R region of the long terminal repeat (HIV-1 promoter region, LTR), promoting both paused polymerases and increased efficiency of CRISPR/Cas9 editing in infected cells. This implies that gene editing may be best performed under a repressed transcriptional state. Conclusions Collectively, our results indicate that F07#13, which can terminate RNA Polymerase II at distinct sites, can generate scaffold RNAs, which may assemble into specific sets of “RNA Machines” that contribute to gene regulation. It remains to be seen whether these effects can also be seen in various clades that have varying promoter strength, mutant LTRs, and in patient samples. Electronic supplementary material The online version of this article (10.1186/s12977-019-0475-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel O Pinto
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Tristan A Scott
- Center for Gene Therapy, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Catherine DeMarino
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Michelle L Pleet
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Thy T Vo
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Mohammed Saifuddin
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Dmytro Kovalskyy
- Protein Engineering Department, Institute of Molecular Biology and Genetics, UAS, Kiev, Ukraine
| | - James Erickson
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Maria Cowen
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Robert A Barclay
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Chen Zeng
- Department of Physics, The George Washington University, Washington, DC, USA
| | - Marc S Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.,Wits/SA MRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA. .,Laboratory of Molecular Virology, George Mason University, Discovery Hall Room 182, 10900 University Blvd., Manassas, VA, 20110, USA.
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21
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Bon I, Calza L, Musumeci G, Longo S, Bertoldi A, D'Urbano V, Gibellini D, Magistrelli E, Viale PL, Re MC. Impact of Different Antiretroviral Strategies on Total HIV-DNA Level in Virologically Suppressed HIV-1 Infected Patients. Curr HIV Res 2019; 15:448-455. [PMID: 29210661 PMCID: PMC5876918 DOI: 10.2174/1570162x16666171206121026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/02/2017] [Accepted: 11/28/2017] [Indexed: 01/11/2023]
Abstract
Background: Total HIV-DNA load in peripheral blood cell (PBMCs) reflects the global viral reservoir that seems not to be affected by antiretroviral treatment. However, some studies report-ed a different permeability of different drugs in cellular compartments. Objective: To investigate the relation between the amount of total HIV-1 DNA and different treatment strategies. Methods: Total HIV-1 DNA was quantified by real time PCR in PBMCs collected from 161 patients with long-term undetectable HIV-RNA receiving different therapy schedules (3-drug regimens or 2-drug regimen containing Raltegravir as integrase inhibitor). Results: Overall, HIV patients who started therapy with a median pre-ART CD4+ cell count >400 cells/mm3 and HIV viral load of 3 log10 copies/ml, achieved a lower amount of HIV total DNA. No significant correlation was found in DNA size when patients were stratified on the basis of different therapeutic protocols. However, HIV DNA load analysis, when only performed in HIV patients with a median pre-ART CD4+ cell count >200 cells/mm3 and HIV viral load < 3 log10 copies/ml, showed a significative DNA decrease in Raltegravir treated group with respect to the NNRTIs-treated group. Conclusion: The data emphasize that HIV-DNA level represents a predictive factor in long-term sup-pressive therapy patients. In addition, the diminished reservoir, only observed in patients treated with the NRTI-sparing regimen RAL plus PI/r before immunological and virological derangement, sug-gests that latest generation drugs, such as integrase inhibitors, might represent an optimal chance in the management of HIV infection.
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Affiliation(s)
- Isabella Bon
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Leonardo Calza
- Unit of Infectious Diseases, Department of Medical and Surgical Sciences, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Giuseppina Musumeci
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Serena Longo
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Alessia Bertoldi
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Vanessa D'Urbano
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Davide Gibellini
- Unit of Microbiology Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Eleonora Magistrelli
- Unit of Infectious Diseases, Department of Medical and Surgical Sciences, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Pier Luigi Viale
- Unit of Infectious Diseases, Department of Medical and Surgical Sciences, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Maria Carla Re
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy.,Interuniversity Consortium, National Institute of Biostructures and Biosystems (INBB), Rome, Italy
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22
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Ma L, Cao X, Wang H, Lu K, Wang Y, Tu C, Dai Y, Meng Y, Li Y, Yu P, Man S, Diao A. Discovery of Myricetin as a Potent Inhibitor of Human Flap Endonuclease 1, Which Potentially Can Be Used as Sensitizing Agent against HT-29 Human Colon Cancer Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1656-1665. [PMID: 30694659 DOI: 10.1021/acs.jafc.8b05447] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Human flap endonuclease 1 (hFEN1) is instrumental in DNA replication and repair. It is able to cleave the 5' single-stranded protrusion (also known as 5' flap) resulting from strand displacement reactions. In light of its crucial functions, hFEN1 is now deemed as a nontrivial target in the DNA damage response system for anticancer drug development. Herein, we report that myricetin and some natural flavonoids are able to inhibit hFEN1. Structure-activity relationship, inhibitory mechanisms, molecular docking, and cancer cell-based assays have been performed. Our original findings expand the activity of flavonoids and may pave the way for flavonoid-assisted targeted cancer therapy.
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Affiliation(s)
- Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Xiuqi Cao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Haiyue Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Kui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Ying Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Chunhao Tu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Yujie Dai
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Yuanyuan Meng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Yuyin Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Peng Yu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Shuli Man
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
| | - Aipo Diao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology (MOE), Tianjin Key Laboratory of Industrial Microbiology, School of Biotechnology , Tianjin University of Science & Technology , Tianjin 300457 , China
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23
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Akher FB, Farrokhzadeh A, Honarparvar B. Effect of substituent and π-stacking interaction on the metal chelation ability of 7-subestituted 2-oxyisoquinoline-1,3(2H,4H)-diones as an HIV integrase inhibitor: A DFT study. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Jentsch NG, Hume JD, Crull EB, Beauti SM, Pham AH, Pigza JA, Kessl JJ, Donahue MG. Quinolines from the cyclocondensation of isatoic anhydride with ethyl acetoacetate: preparation of ethyl 4-hydroxy-2-methylquinoline-3-carboxylate and derivatives. Beilstein J Org Chem 2018; 14:2529-2536. [PMID: 30344776 PMCID: PMC6178280 DOI: 10.3762/bjoc.14.229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/04/2018] [Indexed: 01/25/2023] Open
Abstract
A convenient two-step synthesis of ethyl 4-hydroxy-2-methylquinoline-3-carboxylate derivatives has been developed starting from commercially available 2-aminobenzoic acids. In step 1, the anthranilic acids are smoothly converted to isatoic anhydrides using solid triphosgene in THF. In step 2, the anhydride electrophiles are reacted with the sodium enolate of ethyl acetoacetate, generated from sodium hydroxide, in warm N,N-dimethylacetamide resulting in the formation of substituted quinolines. A degradation-build-up strategy of the ethyl ester at the 3-position allowed for the construction of the α-hydroxyacetic acid residue required for the synthesis of key arylquinolines involved in an HIV integrase project.
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Affiliation(s)
- Nicholas G Jentsch
- Department of Chemistry and Biochemistry, University of Southern Mississippi, 118 College Drive #5043, Hattiesburg, MS 39406, USA
| | - Jared D Hume
- Department of Chemistry and Biochemistry, University of Southern Mississippi, 118 College Drive #5043, Hattiesburg, MS 39406, USA
| | - Emily B Crull
- Department of Chemistry and Biochemistry, University of Southern Mississippi, 118 College Drive #5043, Hattiesburg, MS 39406, USA
| | - Samer M Beauti
- Department of Chemistry and Biochemistry, University of Southern Mississippi, 118 College Drive #5043, Hattiesburg, MS 39406, USA
| | - Amy H Pham
- Department of Chemistry and Biochemistry, University of Southern Mississippi, 118 College Drive #5043, Hattiesburg, MS 39406, USA
| | - Julie A Pigza
- Department of Chemistry and Biochemistry, University of Southern Mississippi, 118 College Drive #5043, Hattiesburg, MS 39406, USA
| | - Jacques J Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, 118 College Drive #5043, Hattiesburg, MS 39406, USA
| | - Matthew G Donahue
- Department of Chemistry and Biochemistry, University of Southern Mississippi, 118 College Drive #5043, Hattiesburg, MS 39406, USA
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25
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Jentsch NG, Hart AP, Hume JD, Sun J, McNeely KA, Lama C, Pigza JA, Donahue MG, Kessl JJ. Synthesis and Evaluation of Aryl Quinolines as HIV-1 Integrase Multimerization Inhibitors. ACS Med Chem Lett 2018; 9:1007-1012. [PMID: 30344908 DOI: 10.1021/acsmedchemlett.8b00269] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/14/2018] [Indexed: 12/25/2022] Open
Abstract
HIV-1 integrase multimerization inhibitors have recently been established as an effective class of antiretroviral agents due to their potent ability to inhibit viral replication. Specifically, quinoline-based inhibitors have been shown to effectively impair HIV-1 replication, highlighting the importance of these heterocyclic scaffolds. Pursuant of our endeavors to further develop a library of quinoline-based candidates, we have implemented a structure-activity relationship study of trisubstituted 4-arylquinoline scaffolds that examined the integrase multimerization properties of substitution patterns at the 4-position of the quinoline. Compounds consisting of substituted phenyl rings, heteroaromatics, or polycyclic moieties were examined utilizing an integrase aberrant multimerization in vitro assay. para-Chloro-4-phenylquinoline 11b and 2,3-benzo[b][1,4]dioxine 15f showed noteworthy EC50 values of 0.10 and 0.08 μM, respectively.
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Affiliation(s)
- Nicholas G. Jentsch
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Alison P. Hart
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Jared D. Hume
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Jian Sun
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Kaitlin A. McNeely
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Chiyang Lama
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Julie A. Pigza
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Matthew G. Donahue
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
| | - Jacques J. Kessl
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States
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26
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Recent advances in the discovery of small-molecule inhibitors of HIV-1 integrase. Future Sci OA 2018; 4:FSO338. [PMID: 30416746 PMCID: PMC6222271 DOI: 10.4155/fsoa-2018-0060] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022] Open
Abstract
AIDS caused by the infection of HIV is a prevalent problem today. Rapid development of drug resistance to existing drug classes has called for the discovery of new targets. Within the three major enzymes (i.e., HIV-1 protease, HIV-1 reverse transcriptase and HIV-1 integrase [IN]) of the viral replication cycle, HIV-1 IN has been of particular interest due to the absence of human cellular homolog. HIV-1 IN catalyzes the integration of viral genetic material with the host genome, a key step in the viral replication process. Several novel classes of HIV IN inhibitors have been explored by targeting different sites on the enzyme. This review strives to provide readers with updates on the recent developments of HIV-1 IN inhibitors. AIDS is an epidemic disease that endangers the lives of millions of people across the world. The AIDS virus, also known as HIV, has developed resistance to the majority of available drugs on the market, thus requiring the need for new drugs. HIV integrase is one of the key viral enzymes required for viral cell proliferation. Since there is no similar enzyme in the human body, major emphasis is being made to develop therapeutics for this novel target. The drugs that are at various stages of development for this target are reviewed here.
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27
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Silvestri I, Lyu H, Fata F, Boumis G, Miele AE, Ardini M, Ippoliti R, Bellelli A, Jadhav A, Lea WA, Simeonov A, Cheng Q, Arnér ESJ, Thatcher GR, Petukhov PA, Williams DL, Angelucci F. Fragment-Based Discovery of a Regulatory Site in Thioredoxin Glutathione Reductase Acting as "Doorstop" for NADPH Entry. ACS Chem Biol 2018; 13:2190-2202. [PMID: 29800515 PMCID: PMC6905387 DOI: 10.1021/acschembio.8b00349] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Members of the FAD/NAD-linked reductase family are recognized as crucial targets in drug development for cancers, inflammatory disorders, and infectious diseases. However, individual FAD/NAD reductases are difficult to inhibit in a selective manner with off-target inhibition reducing usefulness of identified compounds. Thioredoxin glutathione reductase (TGR), a high molecular weight thioredoxin reductase-like enzyme, has emerged as a promising drug target for the treatment of schistosomiasis, a parasitosis afflicting more than 200 million people. Taking advantage of small molecules selected from a high-throughput screen and using X-ray crystallography, functional assays, and docking studies, we identify a critical secondary site of the enzyme. Compounds binding at this site interfere with well-known and conserved conformational changes associated with NADPH reduction, acting as a doorstop for cofactor entry. They selectively inhibit TGR from Schistosoma mansoni and are active against parasites in culture. Since many members of the FAD/NAD-linked reductase family have similar catalytic mechanisms, the unique mechanism of inhibition identified in this study for TGR broadly opens new routes to selectively inhibit homologous enzymes of central importance in numerous diseases.
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Affiliation(s)
- Ilaria Silvestri
- Dept. of Life, Health and Environmental Sciences, University of L’Aquila, Italy,These authors contributed equally
| | - Haining Lyu
- Dept. of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL USA,These authors contributed equally
| | - Francesca Fata
- Dept. of Life, Health and Environmental Sciences, University of L’Aquila, Italy
| | - Giovanna Boumis
- Dept. of Biochemical Sciences, Sapienza University of Rome, Italy
| | - Adriana E. Miele
- Dept. of Biochemical Sciences, Sapienza University of Rome, Italy,UMR5246 ICBMS – CNRS – UCBL, Université de Lyon, France
| | - Matteo Ardini
- Dept. of Life, Health and Environmental Sciences, University of L’Aquila, Italy
| | - Rodolfo Ippoliti
- Dept. of Life, Health and Environmental Sciences, University of L’Aquila, Italy
| | - Andrea Bellelli
- Dept. of Biochemical Sciences, Sapienza University of Rome, Italy
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Wendy A. Lea
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA,Current address: The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Qing Cheng
- Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Elias S. J. Arnér
- Dept. of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Gregory R. Thatcher
- Dept. of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL USA
| | - Pavel A. Petukhov
- Dept. of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL USA
| | - David L. Williams
- Dept. of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL USA,Senior authors,To whom correspondence should be addressed: David L. Williams (), Francesco Angelucci ()
| | - Francesco Angelucci
- Dept. of Life, Health and Environmental Sciences, University of L’Aquila, Italy,Senior authors,To whom correspondence should be addressed: David L. Williams (), Francesco Angelucci ()
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28
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Zhao XZ, Métifiot M, Kiselev E, Kessl JJ, Maddali K, Marchand C, Kvaratskhelia M, Pommier Y, Burke TR. HIV-1 Integrase-Targeted Short Peptides Derived from a Viral Protein R Sequence. Molecules 2018; 23:molecules23081858. [PMID: 30049955 PMCID: PMC6222646 DOI: 10.3390/molecules23081858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/18/2018] [Accepted: 07/23/2018] [Indexed: 01/28/2023] Open
Abstract
HIV-1 integrase (IN) inhibitors represent a new class of highly effective anti-AIDS therapeutics. Current FDA-approved IN strand transfer inhibitors (INSTIs) share a common mechanism of action that involves chelation of catalytic divalent metal ions. However, the emergence of IN mutants having reduced sensitivity to these inhibitors underlies efforts to derive agents that antagonize IN function by alternate mechanisms. Integrase along with the 96-residue multifunctional accessory protein, viral protein R (Vpr), are both components of the HIV-1 pre-integration complex (PIC). Coordinated interactions within the PIC are important for viral replication. Herein, we report a 7-mer peptide based on the shortened Vpr (69–75) sequence containing a biotin group and a photo-reactive benzoylphenylalanyl residue, and which exhibits low micromolar IN inhibitory potency. Photo-crosslinking experiments have indicated that the peptide directly binds IN. The peptide does not interfere with IN-DNA interactions or induce higher-order, aberrant IN multimerization, suggesting a mode of action for the peptide that is distinct from clinically used INSTIs and developmental allosteric IN inhibitors. This compact Vpr-derived peptide may serve as a valuable pharmacological tool to identify a potential new pharmacologic site.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, Center of Cancer Research, Frederick, MD 21702, USA.
| | - Mathieu Métifiot
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Evgeny Kiselev
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jacques J Kessl
- College of Pharmacy and Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA.
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406, USA.
| | - Kasthuraiah Maddali
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Mamuka Kvaratskhelia
- College of Pharmacy and Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA.
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Terrence R Burke
- Chemical Biology Laboratory, Center of Cancer Research, Frederick, MD 21702, USA.
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29
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30
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Ciubotaru M, Musat MG, Surleac M, Ionita E, Petrescu AJ, Abele E, Abele R. The Design of New HIV-IN Tethered Bifunctional Inhibitors Using Multiple Microdomain Targeted Docking. Curr Med Chem 2018; 26:2574-2600. [PMID: 29623824 DOI: 10.2174/0929867325666180406114405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 12/17/2022]
Abstract
Currently, used antiretroviral HIV therapy drugs exclusively target critical groups in the enzymes essential for the viral life cycle. Increased mutagenesis of their genes changes these viral enzymes, which once mutated can evade therapeutic targeting, effects which confer drug resistance. To circumvent this, our review addresses a strategy to design and derive HIV-Integrase (HIV-IN) inhibitors which simultaneously target two IN functional domains, rendering it inactive even if the enzyme accumulates many mutations. First we review the enzymatic role of IN to insert the copied viral DNA into a chromosome of the host T lymphocyte, highlighting its main functional and structural features to be subjected to inhibitory action. From a functional and structural perspective we present all classes of HIV-IN inhibitors with their most representative candidates. For each chosen compound we also explain its mechanism of IN inhibition. We use the recently resolved cryo EM IN tetramer intasome DNA complex onto which we dock various reference IN inhibitory chemical scaffolds such as to target adjacent functional IN domains. Pairing compounds with complementary activity, which dock in the vicinity of a IN structural microdomain, we design bifunctional new drugs which may not only be more resilient to IN mutations but also may be more potent inhibitors than their original counterparts. In the end of our review we propose synthesis pathways to link such paired compounds with enhanced synergistic IN inhibitory effects.
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Affiliation(s)
- Mihai Ciubotaru
- Department of Immunology, Colentina Clinical Hospital Research Center, Bucharest, Romania.,Department of Life and Environmental Physics, National Institute for Physics and Nuclear Engineering Horia Hulubei, Bucharest-Magurele, Romania
| | - Mihaela Georgiana Musat
- Department of Immunology, Colentina Clinical Hospital Research Center, Bucharest, Romania.,Department of Biochemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Marius Surleac
- Department of Bio-informatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Elena Ionita
- Department of Immunology, Colentina Clinical Hospital Research Center, Bucharest, Romania.,Department of Life and Environmental Physics, National Institute for Physics and Nuclear Engineering Horia Hulubei, Bucharest-Magurele, Romania
| | - Andrei Jose Petrescu
- Department of Bio-informatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Edgars Abele
- Modern Catalysis Method Mihai Ciubotaru group, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Ramona Abele
- Modern Catalysis Method Mihai Ciubotaru group, Latvian Institute of Organic Synthesis, Riga, Latvia
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31
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Young RJ, Leeson PD. Mapping the Efficiency and Physicochemical Trajectories of Successful Optimizations. J Med Chem 2018; 61:6421-6467. [DOI: 10.1021/acs.jmedchem.8b00180] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Robert J. Young
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul D. Leeson
- Paul Leeson Consulting Ltd., The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K
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32
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Nagarjuna U, Rekha T, Sreenivasulu T, Padmavathi V, Padmaja A. Synthesis of some new pyrrolyl dipyrazoles and pyrrolyl pyrazolyl isoxazoles and biological evaluation as antioxidants. RESEARCH ON CHEMICAL INTERMEDIATES 2018. [DOI: 10.1007/s11164-018-3393-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Lacbay CM, Menni M, Bernatchez JA, Götte M, Tsantrizos YS. Pharmacophore requirements for HIV-1 reverse transcriptase inhibitors that selectively "Freeze" the pre-translocated complex during the polymerization catalytic cycle. Bioorg Med Chem 2018; 26:1713-1726. [PMID: 29478802 DOI: 10.1016/j.bmc.2018.02.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/06/2018] [Accepted: 02/13/2018] [Indexed: 12/20/2022]
Abstract
Reverse transcriptase (RT) is responsible for replicating the HIV-1 genome and is a validated therapeutic target for the treatment of HIV infections. During each cycle of the RT-catalyzed DNA polymerization process, inorganic pyrophosphate is released as the by-product of nucleotide incorporation. Small molecules were identified that act as bioisosteres of pyrophosphate and can selectively freeze the catalytic cycle of HIV-1 RT at the pre-translocated stage of the DNA- or RNA-template-primer-enzyme complex.
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Affiliation(s)
- Cyrus M Lacbay
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Michael Menni
- Department of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
| | - Jean A Bernatchez
- Department of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, 6-020 Katz Group Centre, Edmonton, Alberta T6G 2E1, Canada; Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, Quebec H3A 2B4, Canada
| | - Youla S Tsantrizos
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada; Department of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada.
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34
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Parizadeh N, Alipour E, Soleymani S, Zabihollahi R, Aghasadeghi MR, Hajimahdi Z, Zarghi A. Synthesis of Novel 3-(5-(Alkyl/arylthio)-1,3,4-Oxadiazol-2-yl)-8-Phenylquinolin-4(1H)-One Derivatives as Anti-HIV Agents. PHOSPHORUS SULFUR 2017. [DOI: 10.1080/10426507.2017.1394302] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Niloofar Parizadeh
- Department of Organic Chemistry, Azad University, Tehran North Branch, Tehran, Iran
| | - Eskandar Alipour
- Department of Organic Chemistry, Azad University, Tehran North Branch, Tehran, Iran
| | - Sepehr Soleymani
- Hepatitis and AIDS department, Pasteur institute of Iran, Tehran, Iran
| | | | | | - Zahra Hajimahdi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afshin Zarghi
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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35
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Probing Resistance Mutations in Retroviral Integrases by Direct Measurement of Dolutegravir Fluorescence. Sci Rep 2017; 7:14067. [PMID: 29070877 PMCID: PMC5656594 DOI: 10.1038/s41598-017-14564-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/11/2017] [Indexed: 12/12/2022] Open
Abstract
FDA-approved integrase strand transfer inhibitors (raltegravir, elvitegravir and dolutegravir) efficiently inhibit HIV-1 replication. Here, we present fluorescence properties of these inhibitors. Dolutegravir displays an excitation mode particularly dependent on Mg2+ chelation, allowing to directly probe its Mg2+-dependent binding to the prototype foamy virus (PFV) integrase. Dolutegravir-binding studied by both its fluorescence anisotropy and subsequent emission enhancement, strictly requires a preformed integrase/DNA complex, the ten terminal base pairs from the 3′-end of the DNA reactive strand being crucial to optimize dolutegravir-binding in the context of the ternary complex. From the protein side, mutation of any catalytic residue fully abolishes dolutegravir-binding. We also compared dolutegravir-binding to PFV F190Y, G187R and S217K mutants, corresponding to HIV-1 F121Y, G118R and G140S/Q148K mutations that confer low-to-high resistance levels against raltegravir/dolutegravir. The dolutegravir-binding properties derived from fluorescence-based binding assays and drug susceptibilities in terms of catalytic activity, are well correlated. Indeed, dolutegravir-binding to wild-type and F190Y integrases are comparable while strongly compromised with G187R and S217K. Accordingly, the two latter mutants are highly resistant to dolutegravir while F190Y shows only moderate or no resistance. Intrinsic fluorescence properties of dolutegravir are thus particularly suitable for a thorough characterization of both DNA-binding properties of integrase and resistance mutations.
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36
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Structural basis for the potent inhibition of the HIV integrase-LEDGF/p75 protein-protein interaction. J Mol Graph Model 2017; 75:189-198. [PMID: 28582696 DOI: 10.1016/j.jmgm.2017.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/23/2017] [Accepted: 05/24/2017] [Indexed: 11/20/2022]
Abstract
Integrase (IN) constitutes one of the key enzymes involved in the lifecycle of the Human Immunodeficiency Virus (HIV), the etiological agent of AIDS. The biological role of IN strongly depends on the recognition and binding of cellular cofactors belonging to the infected host cell. Thus, the inhibition of the protein-protein interaction (PPI) between IN and cellular cofactors has been envisioned as a promising therapeutic target. In the present work we explore a structure-activity relationship for a set of 14 compounds reported as inhibitors of the PPI between IN and the lens epithelium-derived growth factor (LEDGF/p75). Our results demonstrate that the possibility to adopt the bioactive conformation capable of interacting with the hotspots IN-LEDGF/p75 hotspots residues constitutes a critical feature to obtain a potent inhibition. A ligand efficiency (|Lig-Eff|) quantitative descriptor combining both interaction energetics and conformational requirements was developed and correlated with the reported biological activity. Our results contribute to the rational development of IN-LEDGF/p75 interaction inhibitors providing a solid quantitative structure-activity relationship aimed for the screening of new IN-LEDGF/p75 interaction inhibitors.
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Xue P, Lu HH, Zhu YY, Ju XL, Pannecouque C, Zheng XJ, Liu GY, Zhang XL, Gu SX. Design and synthesis of hybrids of diarylpyrimidines and diketo acids as HIV-1 inhibitors. Bioorg Med Chem Lett 2017; 27:1640-1643. [PMID: 28314598 DOI: 10.1016/j.bmcl.2017.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 02/22/2017] [Accepted: 03/06/2017] [Indexed: 10/20/2022]
Abstract
Based on the strategy of molecular hybridization, diketo acid fragment as a classical phamacophore of integrase inhibitors was introduced to reverse transcriptase inhibitors diarylpyrimidines to design a series of diarylpyrimidine-diketo acid hybrids (DAPY-DKAs). The target molecules 10b and 11b showed inhibitory activities against WT HIV-1 with EC50 values of 0.18μM and 0.14μM, respectively. And the results of molecular docking demonstrated the potential binding mode and revealed that the DKA moiety and its ester could both be tolerated in the nonnucleoside binding site (NNBS) of HIV-1 RT.
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Affiliation(s)
- Ping Xue
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Huan-Huan Lu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Xiu-Lian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Christophe Pannecouque
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Xiao-Jiao Zheng
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Gen-Yan Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Xiu-Lan Zhang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Shuang-Xi Gu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China.
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38
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Obydennov DL, Khammatova LR, Sosnovskikh VY. Synthesis of ethyl 4-(isoxazol-4-yl)-2,4-dioxobutanoates from ethyl 5-aroyl-4-pyrone-2-carboxylates and hydroxylamine. MENDELEEV COMMUNICATIONS 2017. [DOI: 10.1016/j.mencom.2017.03.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Sun Y, Xu W, Fan N, Sun X, Ning X, Ma L, Liu J, Wang X. Design, synthesis and biological evaluation of (E)-3,4-dihydroxystyryl 4-acylaminophenethyl sulfone, sulfoxide derivatives as dual inhibitors of HIV-1 CCR5 and integrase. Bioorg Med Chem 2016; 25:1076-1084. [PMID: 28082070 DOI: 10.1016/j.bmc.2016.12.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 11/26/2016] [Accepted: 12/16/2016] [Indexed: 01/19/2023]
Abstract
Aiming at the limited effectiveness of current clinical therapeutic effect of AIDS, novel series of compounds bearing (E)-3,4-dihydroxystyryl sulfone (or sulfoxide) and anilide fragments were designed and synthesized as dual inhibitors of HIV-1 CCR5/IN. The biological results indicated that several target compounds showed inhibitory activity against HIV-1 Bal (R5) infection in TZM-bl cells. Besides targeting the chemokine receptor on the host cell surface, they also displayed binding affinities with HIV-1 integrase using the surface plasmon resonance (SPR) binding assays. Molecular docking studies have inferred the possible binding mode of target compounds against integrase. These data demonstrate that the structure of (E)-3,4-dihydroxystyryl sulfone and sulfoxide derivatives have the potential to derive potent dual inhibitors of HIV-1 Integrase and CCR5.
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Affiliation(s)
- Yixing Sun
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Weisi Xu
- State Key Laboratory of Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center of Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China
| | - Ningning Fan
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xuefeng Sun
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xianling Ning
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Liying Ma
- State Key Laboratory of Infection Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center of Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Changping District, Beijing 102206, China.
| | - Junyi Liu
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
| | - Xiaowei Wang
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
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40
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Obydennov DL, Pan’kina EO, Sosnovskikh VY. Synthesis of Diketohexenoic Acid Derivatives by Alkenylation of Indoles and Pyrroles with 4-Pyrones. J Org Chem 2016; 81:12532-12539. [DOI: 10.1021/acs.joc.6b02364] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Dmitrii L. Obydennov
- Department of Chemistry,
Institute of Natural Sciences, Ural Federal University, 620000 Ekaterinburg, Russian Federation
| | - Ekaterina O. Pan’kina
- Department of Chemistry,
Institute of Natural Sciences, Ural Federal University, 620000 Ekaterinburg, Russian Federation
| | - Vyacheslav Y. Sosnovskikh
- Department of Chemistry,
Institute of Natural Sciences, Ural Federal University, 620000 Ekaterinburg, Russian Federation
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Gotsko MD, Sobenina LN, Tomilin DN, Markova MV, Ushakov IA, Vakul’skaya TI, Khutsishvili SS, Trofimov BA. Pyrrole acetylenecarbaldehydes: an entry to a novel class of functionalized pyrroles. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.09.079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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42
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Zhang FH, Debnath B, Xu ZL, Yang LM, Song LR, Zheng YT, Neamati N, Long YQ. Discovery of novel 3-hydroxypicolinamides as selective inhibitors of HIV-1 integrase-LEDGF/p75 interaction. Eur J Med Chem 2016; 125:1051-1063. [PMID: 27810592 DOI: 10.1016/j.ejmech.2016.10.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 09/27/2016] [Accepted: 10/19/2016] [Indexed: 12/27/2022]
Abstract
Currently, three HIV-1 integrase (IN) active site-directed inhibitors are in clinical use for the treatment of HIV infection. However, emergence of drug resistance mutations have limited the promise of a long-term cure. As an alternative, allosteric inhibition of IN activity has drawn great attention and several of such inhibitors are under early stage clinical development. Specifically, inhibitors of IN and the cellular cofactor LEDGF/p75 remarkably diminish proviral integration in cells and deliver a potent reduction in viral replicative capacity. Distinct from the extensively studied 2-(quinolin-3-yl) acetic acid or 1H-indol-3-yl-2-hydroxy-4-oxobut-2-enoic acid chemotypes, this study discloses a new class of selective IN-LEDGF/p75 inhibitors without the carboxylic acid functionality. More significantly, 3-hydroxypicolinamides also show low micromolar inhibition against IN dimerization, providing novel dual IN inhibitors with in vitro therapeutically selective antiviral effect for further development. Finally, our shape-based ROCS pharmacophore model of the 3-hydroxypicolinamide class of compounds provides a new insight into the binding mode of these novel IN-LEDGF/p75 inhibitors.
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Affiliation(s)
- Feng-Hua Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Bikash Debnath
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-2800, USA
| | - Zhong-Liang Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Liu-Meng Yang
- Laboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li-Rui Song
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yong-Tang Zheng
- Laboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-2800, USA.
| | - Ya-Qiu Long
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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43
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Corona A, di Leva FS, Rigogliuso G, Pescatori L, Madia VN, Subra F, Delelis O, Esposito F, Cadeddu M, Costi R, Cosconati S, Novellino E, di Santo R, Tramontano E. New insights into the interaction between pyrrolyl diketoacids and HIV-1 integrase active site and comparison with RNase H. Antiviral Res 2016; 134:236-243. [PMID: 27659398 DOI: 10.1016/j.antiviral.2016.09.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/16/2016] [Accepted: 09/19/2016] [Indexed: 12/18/2022]
Abstract
HIV-1 integrase (IN) inhibitors are one of the most recent innovations in the treatment of HIV infection. The selection of drug resistance viral strains is however a still open issue requiring constant efforts to identify new anti-HIV-1 drugs. Pyrrolyl diketo acid (DKA) derivatives inhibit HIV-1 replication by interacting with the Mg2+ cofactors within the HIV-1 IN active site or within the HIV-1 reverse-transcriptase associated ribonuclease H (RNase H) active site. While the interaction mode of pyrrolyl DKAs with the RNase H active site has been recently reported and substantiated by mutagenesis experiments, their interaction within the IN active site still lacks a detailed understanding. In this study, we investigated the binding mode of four pyrrolyl DKAs to the HIV-1 IN active site by molecular modeling coupled with site-directed mutagenesis studies showing that the DKA pyrrolyl scaffold primarily interacts with the IN amino residues P145, Q146 and Q148. Importantly, the tested DKAs demonstrated good effectiveness against HIV-1 Raltegravir resistant Y143A and N155H INs, thus showing an interaction pattern with relevant differences if compared with the first generation IN inhibitors. These data provide precious insights for the design of new HIV inhibitors active on clinically selected Raltegravir resistant variants. Furthermore, this study provides new structural information to modulate IN and RNase H inhibitory activities for development of dual-acting anti-HIV agents.
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Affiliation(s)
- Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy
| | - Francesco Saverio di Leva
- Department of Pharmacy, University of Naples "Federico II", Via Domenico Montesano, 49 80131, Naples, Italy
| | - Giuseppe Rigogliuso
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy; LBPA, ENS Cachan, CNRS, 61 Avenue du président Wilson, 94235, Cachan Cedex, France
| | - Luca Pescatori
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Valentina Noemi Madia
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Frederic Subra
- LBPA, ENS Cachan, CNRS, 61 Avenue du président Wilson, 94235, Cachan Cedex, France
| | - Olivier Delelis
- LBPA, ENS Cachan, CNRS, 61 Avenue du président Wilson, 94235, Cachan Cedex, France
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy
| | - Marta Cadeddu
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Sandro Cosconati
- DiSTABiF, Seconda Università di Napoli, Via Vivaldi, 43, 81100, Caserta, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", Via Domenico Montesano, 49 80131, Naples, Italy
| | - Roberto di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, "Sapienza" Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria SS554, 09042, Monserrato, Italy.
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44
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Gu SX, Xue P, Ju XL, Zhu YY. Advances in rationally designed dual inhibitors of HIV-1 reverse transcriptase and integrase. Bioorg Med Chem 2016; 24:5007-5016. [PMID: 27658796 DOI: 10.1016/j.bmc.2016.09.025] [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: 08/24/2016] [Revised: 09/09/2016] [Accepted: 09/10/2016] [Indexed: 01/07/2023]
Abstract
Reverse transcriptase (RT) and integrase (IN) are two indispensable enzymes in human immunodeficiency virus type 1 (HIV-1) replication. RT is responsible for the transformation of the single-stranded RNA viral genome into double-stranded DNA, and IN catalyzes the integration of viral DNA into the host DNA. Although highly active antiretroviral therapy (HAART) combining nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs/NtRTIs) with nonnucleoside reverse transcriptase inhibitors (NNRTIs) or protease inhibitors (PIs) could suppress successfully HIV viral load and reduce evidently the mortality of HIV infected people, it involves the difficulty of perfect adherence, and other drawbacks such as viral rebound, toxicities and multi-drug resistances. Recently, rational drug design has become a dominant technique for the development of multi-target drugs. And the rationally designed dual inhibitors of HIV-1 RT and IN have become a hot topic of anti-HIV research. In this review, the advances in rationally designed dual inhibitors of HIV-1 RT and IN were summarized, including structurally diverse inhibitors, their structure-activity relationship (SAR) studies as well as binding mode analysis.
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Affiliation(s)
- Shuang-Xi Gu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, China.
| | - Ping Xue
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, China
| | - Xiu-Lian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073, China
| | - Yuan-Yuan Zhu
- School of Chemistry and Environmental Engineering, Wuhan Institute of Technology, Wuhan 430073, China.
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45
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Liu GN, Luo RH, Zhou Y, Zhang XJ, Li J, Yang LM, Zheng YT, Liu H. Synthesis and Anti-HIV-1 Activity Evaluation for Novel 3a,6a-Dihydro-1H-pyrrolo[3,4-c]pyrazole-4,6-dione Derivatives. Molecules 2016; 21:molecules21091198. [PMID: 27617994 PMCID: PMC6274355 DOI: 10.3390/molecules21091198] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 08/30/2016] [Accepted: 08/30/2016] [Indexed: 12/12/2022] Open
Abstract
The search for new molecular constructs that resemble the critical two-metal binding pharmacophore and the halo-substituted phenyl functionality required for HIV-1 integrase (IN) inhibition represents a vibrant area of research within drug discovery. As reported herein, we have modified our recently disclosed 1-[2-(4-fluorophenyl)ethyl]-pyrrole-2,5-dione scaffolds to design 35 novel compounds with improved biological activities against HIV-1. These new compounds show single-digit micromolar antiviral potencies against HIV-1 and low toxicity. Among of them, compound 9g and 15i had potent anti-HIV-1 activities (EC50 < 5 μM) and excellent therapeutic index (TI, CC50/EC50 > 100). These two compounds have potential as lead compounds for further optimization into clinical anti-HIV-1 agents.
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Affiliation(s)
- Guan-Nan Liu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, Zhejiang, China.
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Rong-Hua Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
| | - Yu Zhou
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Xing-Jie Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
| | - Jian Li
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Liu-Meng Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
| | - Hong Liu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China.
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Exell JC, Thompson MJ, Finger LD, Shaw SJ, Debreczeni J, Ward TA, McWhirter C, Siöberg CLB, Martinez Molina D, Abbott WM, Jones CD, Nissink JWM, Durant ST, Grasby JA. Cellularly active N-hydroxyurea FEN1 inhibitors block substrate entry to the active site. Nat Chem Biol 2016; 12:815-21. [PMID: 27526030 PMCID: PMC5348030 DOI: 10.1038/nchembio.2148] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 05/19/2016] [Indexed: 02/07/2023]
Abstract
The structure-specific nuclease human flap endonuclease-1 (hFEN1) plays a key role in DNA replication and repair and may be of interest as an oncology target. We present the crystal structure of inhibitor-bound hFEN1, which shows a cyclic N-hydroxyurea bound in the active site coordinated to two magnesium ions. Three such compounds had similar IC50 values but differed subtly in mode of action. One had comparable affinity for protein and protein-substrate complex and prevented reaction by binding to active site catalytic metal ions, blocking the necessary unpairing of substrate DNA. Other compounds were more competitive with substrate. Cellular thermal shift data showed that both inhibitor types engaged with hFEN1 in cells, and activation of the DNA damage response was evident upon treatment with inhibitors. However, cellular EC50 values were significantly higher than in vitro inhibition constants, and the implications of this for exploitation of hFEN1 as a drug target are discussed.
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Affiliation(s)
- Jack C Exell
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield, UK
| | - Mark J Thompson
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield, UK
| | - L David Finger
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield, UK
| | - Steven J Shaw
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield, UK
| | - Judit Debreczeni
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, UK
| | - Thomas A Ward
- Bioscience, Oncology Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Alderley Park, Cheshire, UK
| | - Claire McWhirter
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, UK
| | | | | | - W Mark Abbott
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, UK
| | - Clifford D Jones
- Chemistry, Oncology Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Alderley Park, UK
| | - J Willem M Nissink
- Chemistry, Oncology Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, UK
| | - Stephen T Durant
- Bioscience, Oncology Innovative Medicines and Early Development Biotech Unit, Cambridge, UK
| | - Jane A Grasby
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield, UK.,Bioscience, Oncology Innovative Medicines and Early Development Biotech Unit, Cambridge, UK
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Patel PA, Kvaratskhelia N, Mansour Y, Antwi J, Feng L, Koneru P, Kobe MJ, Jena N, Shi G, Mohamed MS, Li C, Kessl JJ, Fuchs JR. Indole-based allosteric inhibitors of HIV-1 integrase. Bioorg Med Chem Lett 2016; 26:4748-4752. [PMID: 27568085 DOI: 10.1016/j.bmcl.2016.08.037] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 11/15/2022]
Abstract
Employing a scaffold hopping approach, a series of allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) have been synthesized based on an indole scaffold. These compounds incorporate the key elements utilized in quinoline-based ALLINIs for binding to the IN dimer interface at the principal LEDGF/p75 binding pocket. The most potent of these compounds displayed good activity in the LEDGF/p75 dependent integration assay (IC50=4.5μM) and, as predicted based on the geometry of the five- versus six-membered ring, retained activity against the A128T IN mutant that confers resistance to many quinoline-based ALLINIs.
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Affiliation(s)
- Pratiq A Patel
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Department of Chemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Nina Kvaratskhelia
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Yara Mansour
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States; Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Janet Antwi
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Lei Feng
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Pratibha Koneru
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Mathew J Kobe
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Nivedita Jena
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Guqin Shi
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Mosaad S Mohamed
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Chenglong Li
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Jacques J Kessl
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States.
| | - James R Fuchs
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States.
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Gil-Farina I, Schmidt M. Interaction of vectors and parental viruses with the host genome. Curr Opin Virol 2016; 21:35-40. [PMID: 27474966 DOI: 10.1016/j.coviro.2016.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 01/31/2023]
Abstract
Viral replication by acquisition of the host cell biology represents a central part of a virus life cycle. Thereby, integration into the host genome constitutes a successful strategy to ensure viral persistence and viruses have developed different mechanisms to integrate and benefit from cell's transcriptional and translational machinery. While lentiviral (e.g. HIV) integration is influenced by the chromatin landscape encountered upon nuclear entry, certain parvoviruses (e.g. AAV) integrate specifically within genomic regions bearing increasingly known sequence motifs. Gene therapy exploits these viral persistence strategies to achieve efficient and safe long-term transgene expression. Here we focus on two widely used vectors and their parental viruses, HIV and AAV, to discuss recent insights into lentiviral vector oncogenicity by alteration of endogenous transcripts as well as the unresolved AAV vectors genotoxic potential.
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Affiliation(s)
- Irene Gil-Farina
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, 69120 Heidelberg, Germany
| | - Manfred Schmidt
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, 69120 Heidelberg, Germany.
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Zhao XZ, Metifiot M, Smith SJ, Maddali K, Marchand C, Hughes SH, Pommier Y, Burke TR. 6,7-Dihydroxyisoindolin-1-one and 7,8-Dihydroxy-3,4-Dihydroisoquinolin- 1(2H)-one Based HIV-1 Integrase Inhibitors. Curr Top Med Chem 2016; 16:435-40. [PMID: 26268341 DOI: 10.2174/1568026615666150813150058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/03/2015] [Accepted: 04/05/2015] [Indexed: 11/22/2022]
Abstract
Integrase (IN) is an essential viral enzyme required for HIV-1 replication, which has been targeted by anti-AIDS therapeutics. Integrase strand transfer inhibitors (INSTIs) represent a new class of antiretroviral agents developed for the treatment of HIV-1 infections. Important structural features that are shared by many INSTIs include a coplanar arrangement of three heteroatoms that chelate two catalytic Mg(2+) ions in the IN active site and a linked halophenyl ring that binds in the hydrophobic pocket formed by the complex of IN with viral DNA. We recently reported bicyclic 6,7-dihydroxyoxoisoindolin-1-one-based IN inhibitors. In the current study, we modified these inhibitors in three ways. First, we increased the spacer length between the metalchelating triad and the halophenyl group. Second, we replaced the indoline [5,6] bicycle with a fused dihydroxyisoquinolinones [6,6] ring system. Finally, we prepared bis-6,7-dihydroxyisoindolin-1-one-4-sulfonamides as dimeric HIV-1 IN inhibitors. These new analogues showed low micromolar inhibitory potency in in vitro HIV-1 integrase assays.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, National Cancer Institute-Frederick, National Institutes of Health, Frederick, MD 21702, USA.
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Pasi M, Mornico D, Volant S, Juchet A, Batisse J, Bouchier C, Parissi V, Ruff M, Lavery R, Lavigne M. DNA minicircles clarify the specific role of DNA structure on retroviral integration. Nucleic Acids Res 2016; 44:7830-47. [PMID: 27439712 PMCID: PMC5027509 DOI: 10.1093/nar/gkw651] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/11/2016] [Indexed: 01/26/2023] Open
Abstract
Chromatin regulates the selectivity of retroviral integration into the genome of infected cells. At the nucleosome level, both histones and DNA structure are involved in this regulation. We propose a strategy that allows to specifically study a single factor: the DNA distortion induced by the nucleosome. This strategy relies on mimicking this distortion using DNA minicircles (MCs) having a fixed rotational orientation of DNA curvature, coupled with atomic-resolution modeling. Contrasting MCs with linear DNA fragments having identical sequences enabled us to analyze the impact of DNA distortion on the efficiency and selectivity of integration. We observed a global enhancement of HIV-1 integration in MCs and an enrichment of integration sites in the outward-facing DNA major grooves. Both of these changes are favored by LEDGF/p75, revealing a new, histone-independent role of this integration cofactor. PFV integration is also enhanced in MCs, but is not associated with a periodic redistribution of integration sites, thus highlighting its distinct catalytic properties. MCs help to separate the roles of target DNA structure, histone modifications and integrase (IN) cofactors during retroviral integration and to reveal IN-specific regulation mechanisms.
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Affiliation(s)
- Marco Pasi
- MMSB UMR5086 University of Lyon I/CNRS, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Damien Mornico
- Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, USR 3756 IP-CNRS, Paris 75015, France
| | - Stevenn Volant
- Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, USR 3756 IP-CNRS, Paris 75015, France
| | - Anna Juchet
- Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, UMR 3569 IP-CNRS, Paris 75015, France
| | - Julien Batisse
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Dpt de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Illkirch 67400, France
| | - Christiane Bouchier
- Institut Pasteur, PF1, Plate-forme Génomique-Pôle Biomics, Citech, Paris 75015, France
| | - Vincent Parissi
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, UMR 5234 CNRS-Université de Bordeaux, Bordeaux 33000, France
| | - Marc Ruff
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Dpt de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Illkirch 67400, France
| | - Richard Lavery
- MMSB UMR5086 University of Lyon I/CNRS, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Marc Lavigne
- Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, UMR 3569 IP-CNRS, Paris 75015, France
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