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Zhang L, Ke D, Li Y, Zhang H, Zhang X, Wang S, Ni S, Peng B, Zeng H, Hou T, Du Y, Pan P, Yu Y, Chen W. Design and synthesis of 7-membered lactam fused hydroxypyridinones as potent metal binding pharmacophores (MBPs) for inhibiting influenza virus PA N endonuclease. Eur J Med Chem 2024; 276:116639. [PMID: 38964259 DOI: 10.1016/j.ejmech.2024.116639] [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: 04/28/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
Since influenza virus RNA polymerase subunit PAN is a dinuclear Mn2+ dependent endonuclease, metal-binding pharmacophores (MBPs) with Mn2+ coordination has been elucidated as a promising strategy to develop PAN inhibitors for influenza treatment. However, few attentions have been paid to the relationship between the optimal arrangement of the donor atoms in MBPs and anti-influenza A virus (IAV) efficacy. Given that, the privileged hydroxypyridinones fusing a seven-membered lactam ring with diverse side chains, chiral centers or cyclic systems were designed and synthesized. A structure-activity relationship study resulted in a hit compound 16l (IC50 = 2.868 ± 0.063 μM against IAV polymerase), the seven-membered lactam ring of which was fused a pyrrolidine ring. Further optimization of the hydrophobic binding groups on 16l afforded a lead compound (R, S)-16s, which exhibited a 64-fold more potent inhibitory activity (IC50 = 0.045 ± 0.002 μM) toward IAV polymerase. Moreover, (R, S)-16s demonstrated a potent anti-IAV efficacy (EC50 = 0.134 ± 0.093 μM) and weak cytotoxicity (CC50 = 15.35 μM), indicating the high selectivity of (R, S)-16s. Although the lead compound (R, S)-16s exhibited a little weaker activity than baloxavir, these findings illustrated the utility of a metal coordination-based strategy in generating novel MBPs with potent anti-influenza activity.
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Affiliation(s)
- Lei Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Di Ke
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, 230601, China
| | - Yuting Li
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, China
| | - Hui Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xi Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Jinhua Institute of Zhejiang University, Jinhua, Zhejiang, 321299, China
| | - Sihan Wang
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, China
| | - Shaokai Ni
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, China
| | - Bo Peng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Huixuan Zeng
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yushen Du
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, China
| | - Peichen Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yongping Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Jinhua Institute of Zhejiang University, Jinhua, Zhejiang, 321299, China; School of Pharmacy, Xinjiang Medical University, Urumqi, 830054, China
| | - Wenteng Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; Jinhua Institute of Zhejiang University, Jinhua, Zhejiang, 321299, China.
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Giannakopoulou E, Akrani I, Mpekoulis G, Frakolaki E, Dimitriou M, Myrianthopoulos V, Vassilaki N, Zoidis G. Novel Pyrazino[1,2- a]indole-1,3(2 H,4 H)-dione Derivatives Targeting the Replication of Flaviviridae Viruses: Structural and Mechanistic Insights. Viruses 2024; 16:1238. [PMID: 39205212 PMCID: PMC11360281 DOI: 10.3390/v16081238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/27/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024] Open
Abstract
Infections with Flaviviridae viruses, such as hepatitis C (HCV), dengue (DENV), and yellow fever (YFV) viruses, are major public health problems worldwide. In the case of HCV, treatment is associated with drug resistance and high costs, while there is no clinically approved therapy for DENV and YFV. Consequently, there is still a need for new chemotherapies with alternative modes of action. We have previously identified novel 2-hydroxypyrazino[1,2-a]indole-1,3(2H,4H)-diones as metal-chelating inhibitors targeting HCV RNA replication. Here, by utilizing a structure-based approach, we rationally designed a second series of compounds by introducing various substituents at the indole core structure and at the imidic nitrogen, to improve specificity against the RNA-dependent RNA polymerase (RdRp). The resulting derivatives were evaluated for their potency against HCV genotype 1b, DENV2, and YFV-17D using stable replicon cell lines. The most favorable substitution was nitro at position 6 of the indole ring (compound 36), conferring EC50 1.6 μM against HCV 1b and 2.57 μΜ against HCV 1a, with a high selectivity index. Compound 52, carrying the acetohydroxamic acid functionality (-CH2CONHOH) on the imidic nitrogen, and compound 78, the methyl-substituted molecule at the position 4 indolediketopiperazine counterpart, were the most effective against DENV and YFV, respectively. Interestingly, compound 36 had a high genetic barrier to resistance and only one resistance mutation was detected, T181I in NS5B, suggesting that the compound target HCV RdRp is in accordance with our predicted model.
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Affiliation(s)
- Erofili Giannakopoulou
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece; (E.G.); (I.A.); (V.M.)
| | - Ifigeneia Akrani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece; (E.G.); (I.A.); (V.M.)
| | - George Mpekoulis
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, GR-11521 Athens, Greece; (G.M.); (M.D.)
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, GR-11521 Athens, Greece; (G.M.); (M.D.)
| | - Marios Dimitriou
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, GR-11521 Athens, Greece; (G.M.); (M.D.)
| | - Vassilios Myrianthopoulos
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece; (E.G.); (I.A.); (V.M.)
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Vas. Sofias Avenue, GR-11521 Athens, Greece; (G.M.); (M.D.)
| | - Grigoris Zoidis
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece; (E.G.); (I.A.); (V.M.)
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3
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Moianos D, Makri M, Prifti GM, Chiotellis A, Pappas A, Woodson ME, Tajwar R, Tavis JE, Zoidis G. N-Hydroxypiridinedione: A Privileged Heterocycle for Targeting the HBV RNase H. Molecules 2024; 29:2942. [PMID: 38931006 PMCID: PMC11206691 DOI: 10.3390/molecules29122942] [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: 05/29/2024] [Revised: 06/12/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
Hepatitis B virus (HBV) remains a global health threat. Ribonuclease H (RNase H), part of the virus polymerase protein, cleaves the pgRNA template during viral genome replication. Inhibition of RNase H activity prevents (+) DNA strand synthesis and results in the accumulation of non-functional genomes, terminating the viral replication cycle. RNase H, though promising, remains an under-explored drug target against HBV. We previously reported the identification of a series of N-hydroxypyridinedione (HPD) imines that effectively inhibit the HBV RNase H. In our effort to further explore the HPD scaffold, we designed, synthesized, and evaluated 18 novel HPD oximes, as well as 4 structurally related minoxidil derivatives and 2 barbituric acid counterparts. The new analogs were docked on the RNase H active site and all proved able to coordinate the two Mg2+ ions in the catalytic site. All of the new HPDs effectively inhibited the viral replication in cell assays exhibiting EC50 values in the low μM range (1.1-7.7 μM) with low cytotoxicity, resulting in selectivity indexes (SI) of up to 92, one of the highest reported to date among HBV RNase H inhibitors. Our findings expand the structure-activity relationships on the HPD scaffold, facilitating the development of even more potent anti-HBV agents.
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Affiliation(s)
- Dimitrios Moianos
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (D.M.); (M.M.); (G.-M.P.)
| | - Maria Makri
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (D.M.); (M.M.); (G.-M.P.)
| | - Georgia-Myrto Prifti
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (D.M.); (M.M.); (G.-M.P.)
| | - Aristeidis Chiotellis
- Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, National Center for Scientific Research “Demokritos”, 15310 Athens, Greece; (A.C.); (A.P.)
| | - Alexandros Pappas
- Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, National Center for Scientific Research “Demokritos”, 15310 Athens, Greece; (A.C.); (A.P.)
| | - Molly E. Woodson
- Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA; (M.E.W.); (R.T.); (J.E.T.)
| | - Razia Tajwar
- Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA; (M.E.W.); (R.T.); (J.E.T.)
| | - John E. Tavis
- Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA; (M.E.W.); (R.T.); (J.E.T.)
| | - Grigoris Zoidis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (D.M.); (M.M.); (G.-M.P.)
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Rossi S, Tudino V, Carullo G, Butini S, Campiani G, Gemma S. Metalloenzyme Inhibitors against Zoonotic Infections: Focus on Leishmania and Schistosoma. ACS Infect Dis 2024; 10:1520-1535. [PMID: 38669567 DOI: 10.1021/acsinfecdis.4c00163] [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] [Indexed: 04/28/2024]
Abstract
The term "zoonosis" denotes diseases transmissible among vertebrate animals and humans. These diseases constitute a significant public health challenge, comprising 61% of human pathogens and causing an estimated 2.7 million deaths annually. Zoonoses not only affect human health but also impact animal welfare and economic stability, particularly in low- and middle-income nations. Leishmaniasis and schistosomiasis are two important neglected tropical diseases with a high prevalence in tropical and subtropical areas, imposing significant burdens on affected regions. Schistosomiasis, particularly rampant in sub-Saharan Africa, lacks alternative treatments to praziquantel, prompting concerns regarding parasite resistance. Similarly, leishmaniasis poses challenges with unsatisfactory treatments, urging the development of novel therapeutic strategies. Effective prevention demands a One Health approach, integrating diverse disciplines to enhance diagnostics and develop safer drugs. Metalloenzymes, involved in parasite biology and critical in different biological pathways, emerged in the last few years as useful drug targets for the treatment of human diseases. Herein we have reviewed recent reports on the discovery of inhibitors of metalloenzymes associated with zoonotic diseases like histone deacetylases (HDACs), carbonic anhydrase (CA), arginase, and heme-dependent enzymes.
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Affiliation(s)
- Sara Rossi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Valeria Tudino
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Gabriele Carullo
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Stefania Butini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Giuseppe Campiani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-7346, Iran
| | - Sandra Gemma
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
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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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Schuck B, Brenk R. On the hunt for metalloenzyme inhibitors: Investigating the presence of metal-coordinating compounds in screening libraries and chemical spaces. Arch Pharm (Weinheim) 2024; 357:e2300648. [PMID: 38279543 DOI: 10.1002/ardp.202300648] [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: 11/08/2023] [Revised: 12/20/2023] [Accepted: 12/27/2023] [Indexed: 01/28/2024]
Abstract
Metalloenzymes play vital roles in various biological processes, requiring the search for inhibitors to develop treatment options for diverse diseases. While compound library screening is a conventional approach, the exploration of virtual chemical spaces housing trillions of compounds has emerged as an alternative strategy. In this study, we investigated the suitability of selected screening libraries and chemical spaces for discovering inhibitors of metalloenzymes featuring common ions (Mg2+, Mn2+, and Zn2+). First, metal-coordinating groups from ligands interacting with ions in the Protein Data Bank were extracted. Subsequently, the prevalence of these groups in two focused screening libraries (Life Chemicals' chelator library, comprising 6,428 compounds, and Otava's chelator fragment library, with 1,784 fragments) as well as two chemical spaces (GalaXi and REAL space, containing billions of virtual products) was investigated. In total, 1,223 metal-coordinating groups were identified, with about a quarter of these groups found within the examined libraries and spaces. Our results indicate that these can serve as valuable starting points for drug discovery targeting metalloenzymes. In addition, this study suggests ways to improve libraries and spaces for better success in finding potential inhibitors for metalloenzymes.
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Affiliation(s)
- Bruna Schuck
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ruth Brenk
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
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Giannakopoulou E, Pardali V, Edwards TC, Woodson M, Tajwar R, Tavis JE, Zoidis G. Identification and assessment of the 1,6-dihydroxy-pyridin-2-one moiety as privileged scaffold for HBV ribonuclease H inhibition. Antiviral Res 2024; 223:105833. [PMID: 38325606 DOI: 10.1016/j.antiviral.2024.105833] [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: 12/18/2023] [Revised: 01/20/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
The Hepatitis B Virus (HBV) ribonuclease H (RNase H) although promising remains an unexploited therapeutic target. HBV RNase H inhibition causes premature termination of viral minus-polarity DNA strands, prevents the synthesis of the viral positive-polarity DNA strand, and causes accumulation of RNA:DNA heteroduplexes within viral capsids. As part of our ongoing research to develop more potent anti-HBV RNase H inhibitors, we designed, synthesized and analyzed a library of 18 novel compounds (17 N-hydroyxpyridinedione (HPD) imine derivatives and 1 barbituric acid analogue) as potential leads for HBV treatment development. In cell assays, fourteen HPDs showed significant anti-HBV activity with EC50s from 1.1 to 2.5 μM and selectivity indices (SI) of up to 58. Three of them exhibited more than 3-fold improvement in the SI over the best previous HPD imine (SI = 13). To gain insight to the interaction between the tested compounds and the active site of HBV RNase H, docking experiments were undertaken. In almost all binding poses, the novel HPDs coordinated both active site Mg2+ ions via their oxygen trident. Furthermore, the novel HPDs displayed high cell permeability and solubility as well as good drug-like properties. These results reveal that HPD imines can be significantly active and selective HBV inhibitors, and that the HPD scaffold merits further development towards anti-HBV agents.
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Affiliation(s)
- Erofili Giannakopoulou
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771, Athens, Greece
| | - Vasiliki Pardali
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771, Athens, Greece
| | - Tiffany C Edwards
- Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, 63104, United States
| | - Molly Woodson
- Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, 63104, United States
| | - Razia Tajwar
- Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, 63104, United States
| | - John E Tavis
- Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, 63104, United States
| | - Grigoris Zoidis
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771, Athens, Greece.
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Zhang L, Yang Y, Yang Y, Xiao Z. Discovery of Novel Metalloenzyme Inhibitors Based on Property Characterization: Strategy and Application for HDAC1 Inhibitors. Molecules 2024; 29:1096. [PMID: 38474606 DOI: 10.3390/molecules29051096] [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: 11/30/2023] [Revised: 02/17/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Metalloenzymes are ubiquitously present in the human body and are relevant to a variety of diseases. However, the development of metalloenzyme inhibitors is limited by low specificity and poor drug-likeness associated with metal-binding fragments (MBFs). A generalized drug discovery strategy was established, which is characterized by the property characterization of zinc-dependent metalloenzyme inhibitors (ZnMIs). Fifteen potential Zn2+-binding fragments (ZnBFs) were identified, and a customized pharmacophore feature was defined based on these ZnBFs. The customized feature was set as a required feature and applied to a search for novel inhibitors for histone deacetylase 1 (HDAC1). Ten potential HDAC1 inhibitors were recognized, and one of them (compound 9) was a known potent HDAC1 inhibitor. The results demonstrated the effectiveness of our strategy to identify novel inhibitors for zinc-dependent metalloenzymes.
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Affiliation(s)
- Lu Zhang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin 300011, China
| | - Yajun Yang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ying Yang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zhiyan Xiao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Digestive Health, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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