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D’Orsi R, Funicello M, Laurita T, Lupattelli P, Berti F, Chiummiento L. The Pseudo-Symmetric N-benzyl Hydroxyethylamine Core in a New Series of Heteroarylcarboxyamide HIV-1 Pr Inhibitors: Synthesis, Molecular Modeling and Biological Evaluation. Biomolecules 2021; 11:biom11111584. [PMID: 34827582 PMCID: PMC8615997 DOI: 10.3390/biom11111584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 11/16/2022] Open
Abstract
Here, we report the synthesis, enzyme inhibition and structure–activity relationship studies of a new potent class of HIV-1 protease inhibitors, which contain a pseudo-symmetric hydroxyethylamine core and heteroarylcarboxyamide moieties. The simple synthetic pathway furnished nine compounds in a few steps with high yields. The compounds were designed taking into account our previous results on other series of inhibitors with different substituents at P’ and P’’ and different ways of linking them to the inhibitor core. Potent inhibitory activity was obtained with nanomolar IC50 values measured with a standard fluorimetric test in 100 mM MES buffer, pH 5.5, containing 400 mM NaCl, 1 mM EDTA, 1 mM DTT and 1 mg/ml BSA. Compounds 9a–c, containing the indole ring in P1, exhibited an HIV-1 protease inhibitory activity more powerful than darunavir in the same assay. To obtain molecular insight into the binding properties of these compounds, docking analysis was performed, and their binding properties were also compared.
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Affiliation(s)
- Rosarita D’Orsi
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Maria Funicello
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Teresa Laurita
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Paolo Lupattelli
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Federico Berti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
- Correspondence: (F.B.); (L.C.)
| | - Lucia Chiummiento
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
- Correspondence: (F.B.); (L.C.)
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Skwarecki AS, Nowak MG, Milewska MJ. Amino Acid and Peptide-Based Antiviral Agents. ChemMedChem 2021; 16:3106-3135. [PMID: 34254457 DOI: 10.1002/cmdc.202100397] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Indexed: 01/10/2023]
Abstract
A significant number of antiviral agents used in clinical practice are amino acids, short peptides, or peptidomimetics. Among them, several HIV protease inhibitors (e. g. lopinavir, atazanavir), HCV protease inhibitors (e. g. grazoprevir, glecaprevir), and HCV NS5A protein inhibitors have contributed to a significant decrease in mortality from AIDS and hepatitis. However, there is an ongoing need for the discovery of new antiviral agents and the development of existing drugs; amino acids, both proteinogenic and non-proteinogenic in nature, serve as convenient building blocks for this purpose. The synthesis of non-proteinogenic amino acid components of antiviral agents could be challenging due to the need for enantiomerically or diastereomerically pure products. Herein, we present a concise review of antiviral agents whose structures are based on amino acids of both natural and unnatural origin. Special attention is paid to the synthetic aspects of non-proteinogenic amino acid components of those agents.
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Affiliation(s)
- Andrzej S Skwarecki
- Department of Pharmaceutical Technology and Biochemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| | - Michał G Nowak
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| | - Maria J Milewska
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
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3
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Tramutola F, Armentano MF, Berti F, Chiummiento L, Lupattelli P, D'Orsi R, Miglionico R, Milella L, Bisaccia F, Funicello M. New heteroaryl carbamates: Synthesis and biological screening in vitro and in mammalian cells of wild-type and mutant HIV-protease inhibitors. Bioorg Med Chem 2019; 27:1863-1870. [DOI: 10.1016/j.bmc.2019.03.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/13/2019] [Accepted: 03/19/2019] [Indexed: 01/30/2023]
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4
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Sanusi ZK, Govender T, Maguire GEM, Maseko SB, Lin J, Kruger HG, Honarparvar B. An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant. J Comput Aided Mol Des 2018; 32:459-471. [PMID: 29397520 DOI: 10.1007/s10822-018-0099-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/16/2018] [Indexed: 01/12/2023]
Abstract
The aspartate protease of the human immune deficiency type-1 virus (HIV-1) has become a crucial antiviral target in which many useful antiretroviral inhibitors have been developed. However, it seems the emergence of new HIV-1 PR mutations enhances drug resistance, hence, the available FDA approved drugs show less activity towards the protease. A mutation and insertion designated L38L↑N↑L PR was recently reported from subtype of C-SA HIV-1. An integrated two-layered ONIOM (QM:MM) method was employed in this study to examine the binding affinities of the nine HIV PR inhibitors against this mutant. The computed binding free energies as well as experimental data revealed a reduced inhibitory activity towards the L38L↑N↑L PR in comparison with subtype C-SA HIV-1 PR. This observation suggests that the insertion and mutations significantly affect the binding affinities or characteristics of the HIV PIs and/or parent PR. The same trend for the computational binding free energies was observed for eight of the nine inhibitors with respect to the experimental binding free energies. The outcome of this study shows that ONIOM method can be used as a reliable computational approach to rationalize lead compounds against specific targets. The nature of the intermolecular interactions in terms of the host-guest hydrogen bond interactions is discussed using the atoms in molecules (AIM) analysis. Natural bond orbital analysis was also used to determine the extent of charge transfer between the QM region of the L38L↑N↑L PR enzyme and FDA approved drugs. AIM analysis showed that the interaction between the QM region of the L38L↑N↑L PR and FDA approved drugs are electrostatic dominant, the bond stability computed from the NBO analysis supports the results from the AIM application. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide information that will aid in the design of much improved HIV-1 PR antiviral drugs.
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Affiliation(s)
- Zainab K Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Sibusiso B Maseko
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Johnson Lin
- School of Life Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
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Funicello M, Chiummiento L, Tramutola F, Armentano M, Bisaccia F, Miglionico R, Milella L, Benedetti F, Berti F, Lupattelli P. Synthesis and biological evaluation in vitro and in mammalian cells of new heteroaryl carboxyamides as HIV-protease inhibitors. Bioorg Med Chem 2017; 25:4715-4722. [DOI: 10.1016/j.bmc.2017.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 11/16/2022]
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6
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Sanusi ZK, Govender T, Maguire GEM, Maseko SB, Lin J, Kruger HG, Honarparvar B. Investigation of the binding free energies of FDA approved drugs against subtype B and C-SA HIV PR: ONIOM approach. J Mol Graph Model 2017; 76:77-85. [PMID: 28711760 DOI: 10.1016/j.jmgm.2017.06.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 06/08/2017] [Accepted: 06/09/2017] [Indexed: 01/15/2023]
Abstract
Human immune virus subtype C is the most widely spread HIV subtype in Sub-Sahara Africa and South Africa. A profound structural insight on finding potential lead compounds is therefore necessary for drug discovery. The focus of this study is to rationalize the nine Food and Drugs Administration (FDA) HIV antiviral drugs complexed to subtype B and C-SA PR using ONIOM approach. To achieve this, an integrated two-layered ONIOM model was used to optimize the geometrics of the FDA approved HIV-1 PR inhibitors for subtype B. In our hybrid ONIOM model, the HIV-1 PR inhibitors as well as the ASP 25/25' catalytic active residues were treated at high level quantum mechanics (QM) theory using B3LYP/6-31G(d), and the remaining HIV PR residues were considered using the AMBER force field. The experimental binding energies of the PR inhibitors were compared to the ONIOM calculated results. The theoretical binding free energies (?Gbind) for subtype B follow a similar trend to the experimental results, with one exemption. The computational model was less suitable for C-SA PR. Analysis of the results provided valuable information about the shortcomings of this approach. Future studies will focus on the improvement of the computational model by considering explicit water molecules in the active pocket. We believe that this approach has the potential to provide much improved binding energies for complex enzyme drug interactions.
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Affiliation(s)
- Z K Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - T Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - G E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; School of Chemistry and Physics, University of KwaZulu-Natal, 4001 Durban, South Africa
| | - S B Maseko
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - J Lin
- School of Life Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - H G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
| | - B Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
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Ghosh AK, Osswald HL, Prato G. Recent Progress in the Development of HIV-1 Protease Inhibitors for the Treatment of HIV/AIDS. J Med Chem 2016; 59:5172-208. [PMID: 26799988 PMCID: PMC5598487 DOI: 10.1021/acs.jmedchem.5b01697] [Citation(s) in RCA: 280] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
HIV-1 protease inhibitors continue to play an important role in the treatment of HIV/AIDS, transforming this deadly ailment into a more manageable chronic infection. Over the years, intensive research has led to a variety of approved protease inhibitors for the treatment of HIV/AIDS. In this review, we outline current drug design and medicinal chemistry efforts toward the development of next-generation protease inhibitors beyond the currently approved drugs.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Heather L. Osswald
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Gary Prato
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
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Bonini C, Chiummiento L, Di Blasio N, Funicello M, Lupattelli P, Tramutola F, Berti F, Ostric A, Miertus S, Frecer V, Kong DX. Synthesis and biological evaluation of new simple indolic non peptidic HIV Protease inhibitors: The effect of different substitution patterns. Bioorg Med Chem 2014; 22:4792-802. [DOI: 10.1016/j.bmc.2014.06.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/25/2014] [Accepted: 06/30/2014] [Indexed: 11/30/2022]
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9
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Recent patents and emerging therapeutics for HIV infections: a focus on protease inhibitors. Pharm Pat Anal 2014; 2:513-38. [PMID: 24237127 DOI: 10.4155/ppa.13.33] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The inclusion of protease inhibitors (PIs) in highly active antiretroviral therapy has significantly improved clinical outcomes in HIV-1-infected patients. To date, PIs are considered to be the most important therapeutic agents for the treatment of HIV infections. Despite high anti-HIV-1 potency, poor oral bioavailability of PIs has been a major concern. For achieving therapeutic concentrations, large doses of PIs are administered, which results in unacceptable systemic toxicities. Such severe and long-term toxicities necessitate the development of safer and potentially promising PIs. Recently, considerable attention has been paid to the development of newer compounds capable of inhibiting wild-type and resistant HIV-1 protease. Some of these PIs have displayed potent HIV-1 protease inhibitory activity. In this review, we have made an attempt to provide an overview on clinically approved and newly developing PIs, and related recent patents in the development of novel PIs.
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Sarabia F, Vivar-García C, García-Ruiz C, Sánchez-Ruiz A, Pino-González MS, García-Castro M, Chammaa S. Exploring the Reactivity of Chiral Glycidic Amides for Their Applications in Synthesis of Bioactive Compounds. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402221] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Chiummiento L, Funicello M, Lupattelli P, Tramutola F. Ligand-free Suzuki coupling of arylboronic acids with methyl (E)-4-bromobut-2-enoate: synthesis of unconventional cores of HIV-1 protease inhibitors. Org Lett 2012; 14:3928-31. [PMID: 22804107 DOI: 10.1021/ol3016786] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An effective ligand-free Suzuki coupling protocol to unite methyl (E)-4-bromobut-2-enoate with several arylboronic acids has been accomplished. Thus, a number of variously functionalized methyl 4-arylcrotonates have been achieved in high to excellent yields under mild conditions. This method enables the preparation of diverse aryl-substituted cores of HIV-1 protease inhibitors.
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Affiliation(s)
- Lucia Chiummiento
- Dipartimento di Chimica Antonio Mario Tamburro, Università Degli Studi della Basilicata, Viale dell'Ateneo Lucano 10, 85100, Potenza, Italy
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12
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Bhattacharya AK, Rana KC, Pannecouque C, De Clercq E. An Efficient Synthesis of a Hydroxyethylamine (HEA) Isostere and Its α-Aminophosphonate and Phosphoramidate Derivatives as Potential Anti-HIV Agents. ChemMedChem 2012; 7:1601-11. [DOI: 10.1002/cmdc.201200271] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 06/12/2012] [Indexed: 11/09/2022]
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13
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Chiummiento L, Funicello M, Lupattelli P, Tramutola F, Berti F, Marino-Merlo F. Synthesis and biological evaluation of novel small non-peptidic HIV-1 PIs: The benzothiophene ring as an effective moiety. Bioorg Med Chem Lett 2012; 22:2948-50. [DOI: 10.1016/j.bmcl.2012.02.046] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/10/2012] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
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Heterocycles in peptidomimetics and pseudopeptides: design and synthesis. Pharmaceuticals (Basel) 2012; 5:297-316. [PMID: 24281380 PMCID: PMC3763636 DOI: 10.3390/ph5030297] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 02/22/2012] [Accepted: 02/28/2012] [Indexed: 11/17/2022] Open
Abstract
This minireview provides a brief outline of the peculiar aspects of the preparation of peptidomimetic and pseudopeptidic structures containing heterocycles. In particular novel tricyclic structures are investigated as potential drugs.
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Ghosh AK, Anderson DD. Tetrahydrofuran, tetrahydropyran, triazoles and related heterocyclic derivatives as HIV protease inhibitors. Future Med Chem 2011; 3:1181-97. [PMID: 21806380 PMCID: PMC3164575 DOI: 10.4155/fmc.11.68] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
HIV/AIDS remains a formidable disease with millions of individuals inflicted worldwide. Although treatment regimens have improved considerably, drug resistance brought on by viral mutation continues to erode their effectiveness. Intense research efforts are currently underway in search of new and improved therapies. This review is concerned with the design of novel HIV-1 protease inhibitors that incorporate heterocyclic scaffolds and which have been reported within the recent literature (2005-2010). Various examples in this review showcase the essential role heterocycles play as scaffolds and bioisosteres in HIV-1 protease inhibitor drug development. This review will hopefully stimulate the widespread application of these heterocycles in the design of other therapeutic agents.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
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