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Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update. J Med Chem 2024; 67:7668-7758. [PMID: 38711345 DOI: 10.1021/acs.jmedchem.3c01825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Laura Hillebrand
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaojun Julia Liang
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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2
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Khalymbadzha IA, Fatykhov RF, Butorin II, Sharapov AD, Potapova AP, Muthipeedika NJ, Zyryanov GV, Melekhin VV, Tokhtueva MD, Deev SL, Kukhanova MK, Mochulskaya NN, Tsurkan MV. Bioinspired Pyrano[2,3- f]chromen-8-ones: Ring C-Opened Analogues of Calanolide A: Synthesis and Anti-HIV-1 Evaluation. Biomimetics (Basel) 2024; 9:44. [PMID: 38248618 PMCID: PMC10813249 DOI: 10.3390/biomimetics9010044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/23/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
We have designed and synthesized a series of bioinspired pyrano[2,3-f]coumarin-based Calanolide A analogs with anti-HIV activity. The design of these new calanolide analogs involved incorporating nitrogen heterocycles or aromatic groups in lieu of ring C, effectively mimicking and preserving their bioactive properties. Three directions for the synthesis were explored: reaction of 5-hydroxy-2,2-dimethyl-10-propyl-2H,8H-pyrano[2,3-f]chromen-8-one with (i) 1,2,4-triazines, (ii) sulfonylation followed by Suzuki cross-coupling with (het)aryl boronic acids, and (iii) aminomethylation by Mannich reaction. Antiviral assay of the synthesized compounds showed that compound 4 has moderate activity against HIV-1 on enzymes and poor activity on the cell model. A molecular docking study demonstrates a good correlation between in silico and in vitro HIV-1 reverse transcriptase (RT) activity of the compounds when docked to the nonnucleoside RT inhibitor binding site, and alternative binding modes of the considered analogs of Calanolide A were established.
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Affiliation(s)
- Igor A. Khalymbadzha
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Ramil F. Fatykhov
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Ilya I. Butorin
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Ainur D. Sharapov
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Anastasia P. Potapova
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Nibin Joy Muthipeedika
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Grigory V. Zyryanov
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Vsevolod V. Melekhin
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
- Department of Medical Biology and Genetics, Ural State Medical University, 620028 Yekaterinburg, Russia
| | - Maria D. Tokhtueva
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Sergey L. Deev
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | | | - Nataliya N. Mochulskaya
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
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Prucha GR, Henry S, Hollander K, Carter ZJ, Spasov KA, Jorgensen WL, Anderson KS. Covalent and noncovalent strategies for targeting Lys102 in HIV-1 reverse transcriptase. Eur J Med Chem 2023; 262:115894. [PMID: 37883896 PMCID: PMC10872499 DOI: 10.1016/j.ejmech.2023.115894] [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: 09/24/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023]
Abstract
Reverse transcriptase (RT) is one of three key proteins responsible for the replication cycle of HIV-1 in the host. Several classes of inhibitors have been developed to target the enzyme, with non-nucleoside reverse transcriptase inhibitors forming first-line treatment. Previously, covalent RT inhibitors have been identified and found to bind irreversibly to commonly mutated residues such as Y181C. In this work we aim to circumvent the issue of NNRTI resistance through targeting K102, which has not yet been identified to confer drug resistance. As reported here, 34 compounds were synthesized and characterized biochemically and structurally with wild-type (WT) HIV-1 RT. Two of these inhibitors demonstrate covalent inhibition as evidenced by protein crystallography, enzyme kinetics, mass spectrometry, and antiviral potency in HIV-1 infected human T-cell assays.
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Affiliation(s)
- Giavana R Prucha
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520-8066, USA
| | - Sean Henry
- Department of Chemistry, Yale University, New Haven, CT, 06520-8107, USA
| | - Klarissa Hollander
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06520-8066, USA
| | - Zachary J Carter
- Department of Chemistry, Yale University, New Haven, CT, 06520-8107, USA
| | - Krasimir A Spasov
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520-8066, USA
| | | | - Karen S Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520-8066, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06520-8066, USA.
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4
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Vanangamudi M, Palaniappan S, Kathiravan MK, Namasivayam V. Strategies in the Design and Development of Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs). Viruses 2023; 15:1992. [PMID: 37896769 PMCID: PMC10610861 DOI: 10.3390/v15101992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
AIDS (acquired immunodeficiency syndrome) is a potentially life-threatening infectious disease caused by human immunodeficiency virus (HIV). To date, thousands of people have lost their lives annually due to HIV infection, and it continues to be a big public health issue globally. Since the discovery of the first drug, Zidovudine (AZT), a nucleoside reverse transcriptase inhibitor (NRTI), to date, 30 drugs have been approved by the FDA, primarily targeting reverse transcriptase, integrase, and/or protease enzymes. The majority of these drugs target the catalytic and allosteric sites of the HIV enzyme reverse transcriptase. Compared to the NRTI family of drugs, the diverse chemical class of non-nucleoside reverse transcriptase inhibitors (NNRTIs) has special anti-HIV activity with high specificity and low toxicity. However, current clinical usage of NRTI and NNRTI drugs has limited therapeutic value due to their adverse drug reactions and the emergence of multidrug-resistant (MDR) strains. To overcome drug resistance and efficacy issues, combination therapy is widely prescribed for HIV patients. Combination antiretroviral therapy (cART) includes more than one antiretroviral agent targeting two or more enzymes in the life cycle of the virus. Medicinal chemistry researchers apply different optimization strategies including structure- and fragment-based drug design, prodrug approach, scaffold hopping, molecular/fragment hybridization, bioisosterism, high-throughput screening, covalent-binding, targeting highly hydrophobic channel, targeting dual site, and multi-target-directed ligand to identify and develop novel NNRTIs with high antiviral activity against wild-type (WT) and mutant strains. The formulation experts design various delivery systems with single or combination therapies and long-acting regimens of NNRTIs to improve pharmacokinetic profiles and provide sustained therapeutic effects.
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Affiliation(s)
- Murugesan Vanangamudi
- Department of Pharmaceutical Chemistry, Amity Institute of Pharmacy, Amity University Madhya Pradesh, Gwalior 474005, Madhya Pradesh, India;
| | - Senthilkumar Palaniappan
- Faculty of Pharmacy, Karpagam Academy of Higher Education, Coimbatore 641021, Tamilnadu, India;
- Center for Active Pharmaceutical Ingredients, Karpagam Academy of Higher Education, Coimbatore 641021, Tamilnadu, India
| | - Muthu Kumaradoss Kathiravan
- Dr. APJ Abdul Kalam Research Lab, SRM College of Pharmacy, SRMIST, Kattankulathur 603203, Tamilnadu, India;
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRMIST, Kattankulathur 603203, Tamilnadu, India
| | - Vigneshwaran Namasivayam
- Pharmaceutical Chemistry, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany
- LIED, University of Lübeck and University Medical Center Schleswig-Holstein, Ratzeburger Allee 160, 23538 Lübeck, Germany
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5
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Homer JA, Xu L, Kayambu N, Zheng Q, Choi EJ, Kim BM, Sharpless KB, Zuilhof H, Dong J, Moses JE. Sulfur fluoride exchange. NATURE REVIEWS. METHODS PRIMERS 2023; 3:58. [PMID: 38873592 PMCID: PMC11171465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Sulfur Fluoride Exchange (SuFEx) is a click reaction par excellence that has revolutionized multiple research fields. In this Primer, we delve into the essential elements of SuFEx operation, catalysis, and SuFExable connective hubs. We also explore the cutting-edge applications of SuFEx in drug development, polymer science, and biochemistry. Additionally, we examine the potential limitations and promising prospects for this versatile click reaction.
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Affiliation(s)
- Joshua A. Homer
- Cancer Center, Cold Spring Harbor Laboratory, 1 Bungtown Road, NY 11724, USA
| | - Long Xu
- Institute of Translational Medicine, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Namitharan Kayambu
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Qinheng Zheng
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Current affiliation: Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Eun Joung Choi
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - Byeong Moon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - K. Barry Sharpless
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- School of Pharmaceutical Science & Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jiajia Dong
- Institute of Translational Medicine, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
| | - John E. Moses
- Cancer Center, Cold Spring Harbor Laboratory, 1 Bungtown Road, NY 11724, USA
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El-Gendi H, Abu-Serie MM, Kamoun EA, Saleh AK, El-Fakharany EM. Statistical optimization and characterization of fucose-rich polysaccharides extracted from pumpkin (Cucurbita maxima) along with antioxidant and antiviral activities. Int J Biol Macromol 2023; 232:123372. [PMID: 36706886 DOI: 10.1016/j.ijbiomac.2023.123372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 01/25/2023]
Abstract
Biologically active phytochemicals from pumpkin reveal versatile medical applications, though little is known about their antiviral activity. The fucose-rich polysaccharide extraction conditions were optimized through Box-Behnken design and purified by column chromatography. The purified fucose-rich polysaccharide was characterized through SEM, FT-IR, 1H NMR, XRD, TGA, and GS-MS. The analysis results revealed an irregular and porous surface of the purified polysaccharide with high fucose, rhamnose, galactose, and glucose contents. The tested fucose-rich polysaccharides revealed significant antioxidant and anti-inflammatory activity at very low concentrations. The purified fucose-rich polysaccharides exerted a broad-spectrum antiviral activity against both DNA and RNA viruses, accompanied by high safety toward normal cells, where the maximum safe doses (EC100) were estimated to be about 3-3.9 mg/mL for both Vero and PBMC cell lines. Treatment of HCV, ADV7, HSV1, and HIV viruses with the purified polysaccharides showed a potent dose-dependent inhibitory activity with IC50 values of 95.475, 20.96, 5.213, and 461.75 μg/mL, respectively. This activity was hypothesized to be through inhibiting the viral entry in HCV infection and inhibiting the reverse transcriptase activity in HIV. The current study firstly reported the antioxidant, anti-inflammatory, and antiviral activities of Cucurbita maxima fucose-rich polysaccharide against several viral infections.
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Affiliation(s)
- Hamada El-Gendi
- Bioprocess Development Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Application (SRTA-City), New Borg El-Arab 21934, Alexandria, Egypt.
| | - Marwa M Abu-Serie
- Medical Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab 21934, Alexandria, Egypt
| | - Elbadawy A Kamoun
- Nanotechnology Research Center (NTRC), The British University in Egypt (BUE), El-Sherouk City, Cairo 11837, Egypt; Polymeric Materials Research Department, Advanced Technology and New Materials Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab 21934, Alexandria, Egypt
| | - Ahmed K Saleh
- Cellulose and Paper Department, National Research Centre, El-Tahrir St., Dokki, Giza, Egypt
| | - Esmail M El-Fakharany
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute GEBRI, City of Scientific Research and Technological Applications, New Borg El-Arab 21934, Alexandria, Egypt.
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Carter ZJ, Hollander K, Spasov KA, Anderson KS, Jorgensen WL. Design, synthesis, and biological testing of biphenylmethyloxazole inhibitors targeting HIV-1 reverse transcriptase. Bioorg Med Chem Lett 2023; 84:129216. [PMID: 36871704 PMCID: PMC10278203 DOI: 10.1016/j.bmcl.2023.129216] [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: 11/17/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
We report non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) using a biphenylmethyloxazole pharmacophore. A crystal structure of benzyloxazole 1 was obtained and suggested the potential viability of biphenyl analogues. In particular, 6a, 6b, and 7 turned out to be potent NNRTIs with low-nanomolar activity in enzyme inhibition and infected T-cell assays, and with low cytotoxicity. Though modeling further suggested that analogues with fluorosulfate and epoxide warheads might provide covalent modification of Tyr188, synthesis and testing did not find evidence for this outcome.
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Affiliation(s)
- Zachary J Carter
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Klarissa Hollander
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520-8066, USA
| | - Krasimir A Spasov
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA
| | - Karen S Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520-8066, USA.
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Carneiro SN, Khasnavis SR, Lee J, Butler TW, Majmudar JD, Am Ende CW, Ball ND. Sulfur(VI) fluorides as tools in biomolecular and medicinal chemistry. Org Biomol Chem 2023; 21:1356-1372. [PMID: 36662157 PMCID: PMC9929716 DOI: 10.1039/d2ob01891h] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023]
Abstract
Recent advances in the synthesis of sulfur(VI)-fluorides has enabled incredible growth in their application in biomolecular chemistry. This review aims to serve as a primer highlighting synthetic strategies toward a diversity of S(VI) fluorides and their application in chemical biology, bioconjugation, and medicinal chemistry.
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Affiliation(s)
- Sabrina N Carneiro
- Department of Chemistry, Pomona College, Claremont, California 91711, USA.
| | - Samuel R Khasnavis
- Department of Chemistry, Pomona College, Claremont, California 91711, USA.
| | - Jisun Lee
- Pfizer Worldwide Research, Development, Groton, Connecticut 06340, USA.
| | - Todd W Butler
- Pfizer Worldwide Research, Development, Groton, Connecticut 06340, USA.
| | - Jaimeen D Majmudar
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA
| | | | - Nicholas D Ball
- Department of Chemistry, Pomona College, Claremont, California 91711, USA.
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Zhou Z, Meng B, An J, Zhao F, Sun Y, Zeng D, Wang W, Gao S, Xia Y, Dun C, De Clercq E, Pannecouque C, Zhan P, Kang D, Liu X. Covalently Targeted Highly Conserved Tyr318 to Improve the Drug Resistance Profiles of HIV-1 NNRTIs: A Proof-of-Concept Study. Int J Mol Sci 2023; 24:ijms24021215. [PMID: 36674730 PMCID: PMC9865928 DOI: 10.3390/ijms24021215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/15/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
This study presents proof of concept for designing a novel HIV-1 covalent inhibitor targeting the highly conserved Tyr318 in the HIV-1 non-nucleoside reverse transcriptase inhibitors binding pocket to improve the drug resistance profiles. The target inhibitor ZA-2 with a fluorosulfate warhead in the structure was found to be a potent inhibitor (EC50 = 11-246 nM) against HIV-1 IIIB and a panel of NNRTIs-resistant strains, being far superior to those of NVP and EFV. Moreover, ZA-2 was demonstrated with lower cytotoxicity (CC50 = 125 µM). In the reverse transcriptase inhibitory assay, ZA-2 exhibited an IC50 value of 0.057 µM with the ELISA method, and the MALDI-TOF MS data demonstrated the covalent binding mode of ZA-2 with the enzyme. Additionally, the molecular simulations have also demonstrated that compounds can form covalent binding to the Tyr318.
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Affiliation(s)
- Zhenzhen Zhou
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Bairu Meng
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Jiaqi An
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Fabao Zhao
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Yanying Sun
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Dan Zeng
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Wenna Wang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Shenghua Gao
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Yu Xia
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Caiyun Dun
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Erik De Clercq
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Peng Zhan
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Dongwei Kang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Shandong University, 44 West Culture Road, Jinan 250012, China
- Correspondence: (D.K.); (X.L.)
| | - Xinyong Liu
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan 250012, China
- China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, Shandong University, 44 West Culture Road, Jinan 250012, China
- Correspondence: (D.K.); (X.L.)
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10
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Deng C, Yan H, Wang J, Liu K, Liu BS, Shi YM. Current scenario on non-nucleoside reverse transcriptase inhibitors (2018-present). ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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Mustafa M, Winum JY. The importance of sulfur-containing motifs in drug design and discovery. Expert Opin Drug Discov 2022; 17:501-512. [PMID: 35193437 DOI: 10.1080/17460441.2022.2044783] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Sulfur-containing functional groups are privileged motifs that occur in various pharmacologically effective substances and several natural products. Various functionalities are found with a sulfur atom at diverse oxidation states, as illustrated by thioether, sulfoxide, sulfone, sulfonamide, sulfamate, and sulfamide functions. They are valuable scaffolds in the field of medicinal chemistry and are part of a large array of approved drugs and clinical candidates. AREA COVERED Herein, the authors review the current research on the development of organosulfur-based drug discovery. This article also covers details of their roles in the new lead compounds reported in the literature over the past five years 2017-2021. EXPERT OPINION Given its prominent role in medicinal chemistry and its importance in drug discovery, sulfur has attracted continuing interest and has been used in the design of various valuable compounds that demonstrate a variety of biological and pharmacological feature activities. Overall, sulfur's role in medicinal chemistry continues to grow. However, many sulfur functionalities remain underused in small-molecule drug discovery and deserve special attention in the armamentarium for treating diverse diseases. Research efforts are also still required for the development of a synthetic methodology for direct access to these functions and late-stage functionalization.
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Affiliation(s)
- Muhamad Mustafa
- IBMM, Univ. Montpellier, CNRS, ENSCM, Montpellier, France.,Department of Medicinal Chemistry, Faculty of Pharmacy, Deraya Unuversity, Minia, Egypt
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12
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Wang Z, Cherukupalli S, Xie M, Wang W, Jiang X, Jia R, Pannecouque C, De Clercq E, Kang D, Zhan P, Liu X. Contemporary Medicinal Chemistry Strategies for the Discovery and Development of Novel HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors. J Med Chem 2022; 65:3729-3757. [PMID: 35175760 DOI: 10.1021/acs.jmedchem.1c01758] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) are a major component of the highly active anti-retroviral therapy (HAART) regimen. However, the occurrence of drug-resistant strains and adverse reactions after long-term usage have inevitably compromised the clinical application of NNRTIs. Therefore, the development of novel inhibitors with distinct anti-resistance profiles and better pharmacological properties is still an enormous challenge. Herein, we summarize state-of-the-art medicinal chemistry strategies for the discovery of potent NNRTIs, such as structure-based design strategies, contemporary computer-aided drug design, covalent-binding strategies, and the application of multi-target-directed ligands. The strategies described here will facilitate the identification of promising HIV-1 NNRTIs.
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Affiliation(s)
- Zhao Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Minghui Xie
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Wenbo Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Ruifang Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China.,China-Belgium Collaborative Research Center for Innovative Antiviral Drugs of Shandong Province, 44 West Culture Road, 250012 Jinan, Shandong, P.R. China
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13
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Frey KM, Bertoletti N, Chan AH, Ippolito JA, Bollini M, Spasov KA, Jorgensen WL, Anderson KS. Structural Studies and Structure Activity Relationships for Novel Computationally Designed Non-nucleoside Inhibitors and Their Interactions With HIV-1 Reverse Transcriptase. Front Mol Biosci 2022; 9:805187. [PMID: 35237658 PMCID: PMC8882919 DOI: 10.3389/fmolb.2022.805187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Reverse transcriptase (RT) from the human immunodeficiency virus continues to be an attractive drug target for antiretroviral therapy. June 2022 will commemorate the 30th anniversary of the first Human Immunodeficiency Virus (HIV) RT crystal structure complex that was solved with non-nucleoside reverse transcriptase inhibitor nevirapine. The release of this structure opened opportunities for designing many families of non-nucleoside reverse transcriptase inhibitors (NNRTIs). In paying tribute to the first RT-nevirapine structure, we have developed several compound classes targeting the non-nucleoside inhibitor binding pocket of HIV RT. Extensive analysis of crystal structures of RT in complex with the compounds informed iterations of structure-based drug design. Structures of seven additional complexes were determined and analyzed to summarize key interactions with residues in the non-nucleoside inhibitor binding pocket (NNIBP) of RT. Additional insights comparing structures with antiviral data and results from molecular dynamics simulations elucidate key interactions and dynamics between the nucleotide and non-nucleoside binding sites.
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Affiliation(s)
- Kathleen M. Frey
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
| | - Nicole Bertoletti
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
| | - Albert H. Chan
- Department of Chemistry, Yale University, New Haven, CT, United States
| | | | - Mariela Bollini
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Krasimir A. Spasov
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
| | | | - Karen S. Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, United States
- *Correspondence: Karen S. Anderson,
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14
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Yi JT, Zhou X, Chen QL, Chen ZD, Lu G, Weng J. Copper-catalyzed direct decarboxylative fluorosulfonylation of aliphatic carboxylic acids. Chem Commun (Camb) 2022; 58:9409-9412. [DOI: 10.1039/d2cc03221j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herein we report two complementary methods for direct decarboxylative fluorosulfonylation of carboxylic acids by the merging of copper catalysis with different N-centered HAT regents.
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Affiliation(s)
- Ji-Tao Yi
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Xiang Zhou
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Qi-Long Chen
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Zhi-Da Chen
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Gui Lu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Jiang Weng
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
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Kim H, Hwang YS, Kim M, Park SB. Recent advances in the development of covalent inhibitors. RSC Med Chem 2021; 12:1037-1045. [PMID: 34355176 DOI: 10.1039/d1md00068c] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/23/2021] [Indexed: 01/03/2023] Open
Abstract
The use of covalent inhibitors in the field of drug discovery has attracted considerable attention in the 2000s. As a result, more than 50 covalent drugs are currently on the market, and numerous covalent drug candidates are now under development. Therefore, interest in covalent drugs is expected to continue in the future. The purpose of this focused review is to provide an understanding of the development of covalent inhibitors by describing their inherent characteristics, possibilities, and limitations based on their mechanistic differences from noncovalent inhibitors. We also introduce the latest covalent warheads that can be applied to the development of potential covalent inhibitors.
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Affiliation(s)
- Hyunsoo Kim
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University Seoul 08826 Korea
| | - Yoon Soo Hwang
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University Seoul 08826 Korea
| | - Mingi Kim
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University Seoul 08826 Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University Seoul 08826 Korea .,Department of Biophysics and Chemical Biology, Seoul National University Seoul 08826 Korea.,SPARK Biopharma, Inc. Seoul 08791 Korea
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