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Bongarzone S, Nadal M, Kaczmarska Z, Machón C, Álvarez M, Albericio F, Coll M. Structure-Driven Discovery of α,γ-Diketoacid Inhibitors Against UL89 Herpesvirus Terminase. ACS OMEGA 2018; 3:8497-8505. [PMID: 31458978 PMCID: PMC6645139 DOI: 10.1021/acsomega.8b01472] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 07/19/2018] [Indexed: 05/27/2023]
Abstract
Human cytomegalovirus (HCMV) is an opportunistic pathogen causing a variety of severe viral infections, including irreversible congenital disabilities. Nowadays, HCMV infection is treated by inhibiting the viral DNA polymerase. However, DNA polymerase inhibitors have several drawbacks. An alternative strategy is to use compounds against the packaging machinery or terminase complex, which is essential for viral replication. Our discovery that raltegravir (1), a human immunodeficiency virus drug, inhibits the nuclease function of UL89, one of the protein subunits of the complex, prompted us to further develop terminase inhibitors. On the basis of the structure of 1, a library of diketoacid (α,γ-DKA and β,δ-DKA) derivatives were synthesized and tested for UL89-C nuclease activity. The mode of action of α,γ-DKA derivatives on the UL89 active site was elucidated by using X-ray crystallography, molecular docking, and in vitro experiments. Our studies identified α,γ-DKA derivative 14 able to inhibit UL89 in vitro in the low micromolar range, making 14 an optimal candidate for further development and virus-infected cell assay.
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Affiliation(s)
- Salvatore Bongarzone
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Marta Nadal
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Zuzanna Kaczmarska
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Cristina Machón
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Mercedes Álvarez
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
- Laboratory
of Organic Chemistry, Faculty of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
- Department
of Organic Chemistry, University of Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Miquel Coll
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- Molecular
Biology Institute of Barcelona (IBMB—CSIC), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
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Banville J, Bouthillier G, Plamondon S, Remillard R, Meanwell NA, Martel A, Walker MA. (Z)-2,2-Dimethyl-5-carboxymethylene-1,3-dioxolan-4-one: a new synthon for the synthesis of α,γ-diketoacid derivatives. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Sun H, Moore C, Dansette PM, Kumar S, Halpert JR, Yost GS. Dehydrogenation of the indoline-containing drug 4-chloro-N-(2-methyl-1-indolinyl)-3-sulfamoylbenzamide (indapamide) by CYP3A4: correlation with in silico predictions. Drug Metab Dispos 2008; 37:672-84. [PMID: 19074530 DOI: 10.1124/dmd.108.022707] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
4-Chloro-N-(2-methyl-1-indolinyl)-3-sulfamoylbenzamide (indapamide), an indoline-containing diuretic drug, has recently been evaluated in a large Phase III clinical trial (ADVANCE) with a fixed-dose combination of an angiotensin-converting enzyme inhibitor, perindopril, and shown to significantly reduce the risks of major vascular toxicities in people with type 2 diabetes. The original metabolic studies of indapamide reported that the indoline functional group was aromatized to indole through a dehydrogenation pathway by cytochromes P450. However, the enzymatic efficiency of indapamide dehydrogenation was not elucidated. A consequence of indoline aromatization is that the product indoles might have dramatically different therapeutic potencies. Thus, studies that characterize dehydrogenation of the functional indoline of indapamide were needed. Here we identified several indapamide metabolic pathways in vitro with human liver microsomes and recombinant CYP3A4 that include the dehydrogenation of indapamide to its corresponding indole form, and also hydroxylation and epoxidation metabolites, as characterized by liquid chromatography/mass spectrometry. Indapamide dehydrogenation efficiency (V(max)/K(m)=204 min/mM) by CYP3A4 was approximately 10-fold greater than that of indoline dehydrogenation. In silico molecular docking of indapamide into two CYP3A4 crystal structures, to evaluate the active site parameters that control dehydrogenation, produced conflicting results about the interactions of Arg212 with indapamide in the active site. These conflicting theories were addressed by functional studies with a CYP3A4R212A mutant enzyme, which showed that Arg212 does not seem to facilitate positioning of indapamide for dehydrogenation. However, the metabolites of indapamide were precisely consistent with in silico predictions of binding orientations using three diverse computer methods to predict drug metabolism pathways.
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Affiliation(s)
- Hao Sun
- Lead Generation Group, Department of Pharmacokinetics, Dynamics, and Drug Metabolism, Global Research and Development, Pfizer, Inc., Groton, Connecticut, USA
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Dayam R, Gundla R, Al-Mawsawi LQ, Neamati N. HIV-1 integrase inhibitors: 2005-2006 update. Med Res Rev 2008; 28:118-54. [PMID: 17979144 DOI: 10.1002/med.20116] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
HIV-1 integrase (IN) catalyzes the integration of proviral DNA into the host genome, an essential step for viral replication. Inhibition of IN catalytic activity provides an attractive strategy for antiretroviral drug design. Currently two IN inhibitors, MK-0518 and GS-9137, are in advanced stages of human clinical trials. The IN inhibitors in clinical evaluation demonstrate excellent antiretroviral efficacy alone or in combination regimens as compared to previously used clinical antiretroviral agents in naive and treatment-experienced HIV-1 infected patients. However, the emergence of viral strains resistant to clinically studied IN inhibitors and the dynamic nature of the HIV-1 genome demand a continued effort toward the discovery of novel inhibitors to keep a therapeutic advantage over the virus. Continued efforts in the field have resulted in the discovery of compounds from diverse chemical classes. In this review, we provide a comprehensive report of all IN inhibitors discovered in the years 2005 and 2006.
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Affiliation(s)
- Raveendra Dayam
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, School of Pharmacy, Los Angeles, California 90089, USA
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Walker MA, Johnson T, Naidu BN, Banville J, Remillard R, Plamondon S, Martel A, Li C, Torri A, Samanta H, Lin Z, Dicker I, Krystal M, Meanwell NA. Benzyl amide-ketoacid inhibitors of HIV-integrase. Bioorg Med Chem Lett 2007; 17:4886-90. [PMID: 17604626 DOI: 10.1016/j.bmcl.2007.06.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Revised: 06/11/2007] [Accepted: 06/12/2007] [Indexed: 11/21/2022]
Abstract
Integrase is one of three enzymes expressed by HIV and represents a validated target for therapy. Previous reports have demonstrated that the diketoacid-based chemotype is a useful starting point for the design of inhibitors of this enzyme. In this study, one of the ketone groups is replaced by a benzylamide resulting in a new potent chemotype. A preliminary SAR study is carried out to investigate the substitution requirements on the phenyl ring and methylene group of the benzylamide.
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Affiliation(s)
- Michael A Walker
- Department of Medicinal Chemistry, Research and Development, Bristol-Myers Squibb, The Richard L Gelb Center for Pharmaceutical Research and Development, Wallingford, CT 06492, USA.
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