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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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2
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Zheng Y, Feng J, Yu Y, Ling M, Song Y, Xie H, Zhang M, Li W, Wang X. Anti-Coronavirus Potential of Polyether Ionophores: The New Application of Veterinary Antibiotics in Livestock. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10640-10654. [PMID: 38661066 DOI: 10.1021/acs.jafc.4c01130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Coronaviruses have consistently posed a major global concern in the field of livestock industry and public health. However, there is currently a lack of efficient drugs with broad-spectrum antiviral activity to address the challenges presented by emerging mutated strains or drug resistance. Additionally, the method for identifying multitarget drugs is also insufficient. Aminopeptidase N (APN) and 3C-like proteinase (3CLpro) represent promising targets for host-directed and virus-directed strategies, respectively, in the development of effective drugs against various coronaviruses. In this study, maduramycin ammonium demonstrated a broad-spectrum antiviral effect by targeting both of the proteins. The binding domains 4 Å from the ligand of both target proteins shared a structural similarity, suggesting that screening and designing drugs based on these domains might exhibit broad-spectrum and highly effective antiviral activity. Furthermore, it was identified that the polyether ionophores' ability to carry zinc ion might be one of the reasons why they were able to target APN and exhibit antiviral effect. The findings of this experiment provide novel perspectives for future drug screening and design, while also offering valuable references for the utilization of polyether ionophores in the management of livestock health.
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Affiliation(s)
- Youle Zheng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Jin Feng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yixin Yu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Min Ling
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yanbin Song
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Haijiao Xie
- Hangzhou Yanqu Information Technology Co., Ltd., Hangzhou, Zhejiang 310003, China
| | - Mengjia Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wentao Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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3
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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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4
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Novakova Z, Tehrani ZA, Jurok R, Motlova L, Kutil Z, Pavlicek J, Shukla S, Choy CJ, Havlinova B, Baranova P, Berkman CE, Kuchar M, Cerny J, Barinka C. Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors. J Chem Inf Model 2024; 64:1030-1042. [PMID: 38224368 PMCID: PMC10865363 DOI: 10.1021/acs.jcim.3c01542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/16/2024]
Abstract
The sulfonamide function is used extensively as a general building block in various inhibitory scaffolds and, more specifically, as a zinc-binding group (ZBG) of metalloenzyme inhibitors. Here, we provide biochemical, structural, and computational characterization of a metallopeptidase in complex with inhibitors, where the mono- and bisubstituted sulfamide functions are designed to directly engage zinc ions of a bimetallic enzyme site. Structural data showed that while monosubstituted sulfamides coordinate active-site zinc ions via the free negatively charged amino group in a canonical manner, their bisubstituted counterparts adopt an atypical binding pattern divergent from expected positioning of corresponding tetrahedral reaction intermediates. Accompanying quantum mechanics calculations revealed that electroneutrality of the sulfamide function is a major factor contributing to the markedly lower potency of bisubstituted compounds by considerably lowering their interaction energy with the enzyme. Overall, while bisubstituted uncharged sulfamide functions can bolster favorable pharmacological properties of a given inhibitor, their use as ZBGs in metalloenzyme inhibitors might be less advantageous due to their suboptimal metal-ligand properties.
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Affiliation(s)
- Zora Novakova
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Zahra Aliakbar Tehrani
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Radek Jurok
- Forensic
Laboratory of Biologically Active Substances, University of Chemistry and Technology Prague, Technická 3, 166 28 Prague 6, Czech Republic
| | - Lucia Motlova
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Zsofia Kutil
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Jiri Pavlicek
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Shivam Shukla
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Cindy J. Choy
- Department
of Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Barbora Havlinova
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Petra Baranova
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Clifford E. Berkman
- Department
of Chemistry, Washington State University, Pullman, Washington 99163, United States
| | - Martin Kuchar
- Forensic
Laboratory of Biologically Active Substances, University of Chemistry and Technology Prague, Technická 3, 166 28 Prague 6, Czech Republic
| | - Jiri Cerny
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
| | - Cyril Barinka
- Institute
of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech
Republic
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5
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Wang YC, Zhang WL, Zhang RH, Liu CH, Zhao YL, Yan GY, Liao SG, Li YJ, Zhou M. The Discovery of Indole-2-carboxylic Acid Derivatives as Novel HIV-1 Integrase Strand Transfer Inhibitors. Molecules 2023; 28:8020. [PMID: 38138510 PMCID: PMC10745497 DOI: 10.3390/molecules28248020] [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: 11/07/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
As an important antiviral target, HIV-1 integrase plays a key role in the viral life cycle, and five integrase strand transfer inhibitors (INSTIs) have been approved for the treatment of HIV-1 infections so far. However, similar to other clinically used antiviral drugs, resistance-causing mutations have appeared, which have impaired the efficacy of INSTIs. In the current study, to identify novel integrase inhibitors, a set of molecular docking-based virtual screenings were performed, and indole-2-carboxylic acid was developed as a potent INSTI scaffold. Indole-2-carboxylic acid derivative 3 was proved to effectively inhibit the strand transfer of HIV-1 integrase, and binding conformation analysis showed that the indole core and C2 carboxyl group obviously chelated the two Mg2+ ions within the active site of integrase. Further structural optimizations on compound 3 provided the derivative 20a, which markedly increased the integrase inhibitory effect, with an IC50 value of 0.13 μM. Binding mode analysis revealed that the introduction of a long branch on C3 of the indole core improved the interaction with the hydrophobic cavity near the active site of integrase, indicating that indole-2-carboxylic acid is a promising scaffold for the development of integrase inhibitors.
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Affiliation(s)
- Yu-Chan Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang 550004, China; (Y.-C.W.); (W.-L.Z.); (R.-H.Z.); (Y.-J.L.)
- Center for Tissue Engineering and Stem Cell Research, Key Laboratory of Regenerative Medicine of Guizhou Province, School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550004, China
- School of Pharmacy, Guizhou Medical University, Guian New District, Guiyang 550025, China; (Y.-L.Z.); (S.-G.L.)
| | - Wen-Li Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang 550004, China; (Y.-C.W.); (W.-L.Z.); (R.-H.Z.); (Y.-J.L.)
- School of Pharmacy, Guizhou Medical University, Guian New District, Guiyang 550025, China; (Y.-L.Z.); (S.-G.L.)
| | - Rong-Hong Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang 550004, China; (Y.-C.W.); (W.-L.Z.); (R.-H.Z.); (Y.-J.L.)
- Center for Tissue Engineering and Stem Cell Research, Key Laboratory of Regenerative Medicine of Guizhou Province, School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550004, China
| | - Chun-Hua Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang 550004, China; (Y.-C.W.); (W.-L.Z.); (R.-H.Z.); (Y.-J.L.)
| | - Yong-Long Zhao
- School of Pharmacy, Guizhou Medical University, Guian New District, Guiyang 550025, China; (Y.-L.Z.); (S.-G.L.)
| | - Guo-Yi Yan
- School of Pharmacy, Xinxiang University, Xinxiang 453000, China;
| | - Shang-Gao Liao
- School of Pharmacy, Guizhou Medical University, Guian New District, Guiyang 550025, China; (Y.-L.Z.); (S.-G.L.)
| | - Yong-Jun Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang 550004, China; (Y.-C.W.); (W.-L.Z.); (R.-H.Z.); (Y.-J.L.)
| | - Meng Zhou
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Medical University, Guiyang 550004, China; (Y.-C.W.); (W.-L.Z.); (R.-H.Z.); (Y.-J.L.)
- School of Pharmacy, Guizhou Medical University, Guian New District, Guiyang 550025, China; (Y.-L.Z.); (S.-G.L.)
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6
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Proj M, Hrast M, Bajc G, Frlan R, Meden A, Butala M, Gobec S. Discovery of a fragment hit compound targeting D-Ala:D-Ala ligase of bacterial peptidoglycan biosynthesis. J Enzyme Inhib Med Chem 2023; 38:387-397. [PMID: 36446617 PMCID: PMC9718554 DOI: 10.1080/14756366.2022.2149745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Bacterial resistance is an increasing threat to healthcare systems, highlighting the need for discovering new antibacterial agents. An established technique, fragment-based drug discovery, was used to target a bacterial enzyme Ddl involved in the biosynthesis of peptidoglycan. We assembled general and focused fragment libraries that were screened in a biochemical inhibition assay. Screening revealed a new fragment-hit inhibitor of DdlB with a Ki value of 20.7 ± 4.5 µM. Binding to the enzyme was confirmed by an orthogonal biophysical method, surface plasmon resonance, making the hit a promising starting point for fragment development.
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Affiliation(s)
- Matic Proj
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Martina Hrast
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Gregor Bajc
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Rok Frlan
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Anže Meden
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia
| | - Matej Butala
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Ljubljana, Slovenia,CONTACT Stanislav Gobec Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Ljubljana, Askerceva 7, 1000Ljubljana, Slovenia
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7
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Gazquez Casals A, Berkowitz AJ, Yu AJ, Waters HE, Schiavone DV, Kapkayeva DM, Morrison LA, Murelli RP. Antiviral activity of amide-appended α-hydroxytropolones against herpes simplex virus-1 and -2. RSC Adv 2023; 13:8743-8752. [PMID: 36936842 PMCID: PMC10016935 DOI: 10.1039/d2ra06749h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/28/2023] [Indexed: 03/17/2023] Open
Abstract
α-Hydroxytropolones (αHTs) have potent antiviral activity against herpes simplex virus-1 and -2 (HSV-1 and HSV-2) in cell culture, including against acyclovir-resistant mutants, and as a result have the potential to be developed as antiviral drugs targeting these viruses. We recently described a convenient final-step amidation strategy to their synthesis, and this was used to generate 57 amide-substituted αHTs that were tested against hepatitis B virus. The following manuscript describes the evaluation of this library against HSV-1, as well as a subset against HSV-2. The structure-function analysis obtained from these studies demonstrates the importance of lipophilicity and rigidity to αHT-based anti-HSV potency, consistent with our prior work on smaller libraries. We used this information to synthesize and test a targeted library of 4 additional amide-appended αHTs. The most potent of this new series had a 50% effective concentration (EC50) for viral inhibition of 72 nM, on par with the most potent αHT antivirals we have found to date. Given the ease of synthesis of amide-appended αHTs, this new class of antiviral compounds and the chemistry to make them should be highly valuable in future anti-HSV drug development.
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Affiliation(s)
- Andreu Gazquez Casals
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine St. Louis MO USA
| | - Alex J Berkowitz
- Department of Chemistry, Brooklyn College, The City University of New York Brooklyn NY USA
- PhD Program in Chemistry, The Graduate Center, The City University of New York New York NY USA
| | - Alice J Yu
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine St. Louis MO USA
| | - Hope E Waters
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine St. Louis MO USA
| | - Daniel V Schiavone
- Department of Chemistry, Brooklyn College, The City University of New York Brooklyn NY USA
- PhD Program in Chemistry, The Graduate Center, The City University of New York New York NY USA
| | - Diana M Kapkayeva
- Department of Chemistry, Brooklyn College, The City University of New York Brooklyn NY USA
| | - Lynda A Morrison
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine St. Louis MO USA
| | - Ryan P Murelli
- Department of Chemistry, Brooklyn College, The City University of New York Brooklyn NY USA
- PhD Program in Chemistry, The Graduate Center, The City University of New York New York NY USA
- PhD Program in Biochemistry, The Graduate Center, The City University of New York New York NY USA
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8
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Lapshin LS, Shchegolkov EV, Burgart YV, Triandafilova GA, Krasnykh OP, Malysheva KO, Saloutin VI. Synthesis of new analgesics based on 4-isopropyl-1-phenyl-3-(trifluoromethyl)pyrazol-5-one. MENDELEEV COMMUNICATIONS 2023. [DOI: 10.1016/j.mencom.2023.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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9
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Sow IS, Gelbcke M, Meyer F, Vandeput M, Marloye M, Basov S, Van Bael MJ, Berger G, Robeyns K, Hermans S, Yang D, Fontaine V, Dufrasne F. Synthesis and biological activity of iron(II), iron(III), nickel(II), copper(II) and zinc(II) complexes of aliphatic hydroxamic acids. J COORD CHEM 2023. [DOI: 10.1080/00958972.2023.2166407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Ibrahima Sory Sow
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Michel Gelbcke
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Franck Meyer
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Marie Vandeput
- Pharmacognosy, Bioanalysis and Drug Discovery Research Unit (RD3-PBM), Faculty of Pharmacy, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Mickael Marloye
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Sergey Basov
- Quantum Solid State Physics, Department of Physics and Astronomy, KU Leuven, Leuven, Belgium
| | - Margriet J. Van Bael
- Quantum Solid State Physics, Department of Physics and Astronomy, KU Leuven, Leuven, Belgium
| | - Gilles Berger
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Koen Robeyns
- Institute of Condensed Matter and Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Sophie Hermans
- Institute of Condensed Matter and Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Dong Yang
- Clinical Laboratory, Shanxi Provincial People’s Hospital, Affiliated of Shanxi Medical University, Taiyuan, China
| | - Véronique Fontaine
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - François Dufrasne
- Microbiology, Bioorganic and Macromolecular Chemistry Unit, Faculty of Pharmacy, Université libre de Bruxelles (ULB), Brussels, Belgium
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10
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Selvaraj C, Rudhra O, Alothaim AS, Alkhanani M, Singh SK. Structure and chemistry of enzymatic active sites that play a role in the switch and conformation mechanism. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:59-83. [PMID: 35534116 DOI: 10.1016/bs.apcsb.2022.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Enzymes, which are biological molecules, are constructed from polypeptide chains, and these molecules are activated through reaction mechanisms. It is the role of enzymes to speed up chemical reactions that are used to build or break down cell structures. Activation energy is reduced by the enzymes' selective binding of substrates in a protected environment. In enzyme tertiary structures, the active sites are commonly situated in a "cleft," which necessitates the diffusion of substrates and products. The amino acid residues of the active site may be far apart in the primary structure owing to the folding required for tertiary structure. Due to their critical role in substrate binding and attraction, changes in amino acid structure at or near the enzyme's active site usually alter enzyme activity. At the enzyme's active site, or where the chemical reactions occur, the substrate is bound. Enzyme substrates are the primary targets of the enzyme's active site, which is designed to assist in the chemical reaction. This chapter elucidates the summary of structure and chemistry of enzymes, their active site features, charges and role of water in the structures to clarify the biochemistry of the enzymes in the depth of atomic features.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - Ondipilliraja Rudhra
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Abdulaziz S Alothaim
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah, Saudi Arabia
| | - Mustfa Alkhanani
- Emergency Service Department, College of Applied Sciences, Al Maarefa University, Riyadh, Saudi Arabia
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
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Bíró L, Buglyó P, Farkas E. Diversity in the Interaction of Amino Acid- and Peptide-Based Hydroxamic Acids with Some Platinum Group Metals in Solution. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030669. [PMID: 35163937 PMCID: PMC8839353 DOI: 10.3390/molecules27030669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 11/29/2022]
Abstract
Complexes that incorporate both ligand(s) and metal(s) exhibiting cytotoxic activity can especially be interesting to develop multifunctional drug molecules with desired activities. In this review, the limited number of solution results collected in our laboratory on the complexes of Pd(II) and two other platinum group metals—the half-sandwich type, [(η6-p-cym)Ru(H2O)3]2+, and [(η5-Cp*)Rh(H2O)3]2+—with hydroxamic acid derivatives of three amino acids, two imidazole analogues, and four small peptides are summarized and evaluated. Unlike the limited number of coordination sites of these metal ions (four and three for Pd(II) and the organometallic cations, respectively), the ligands discussed here offer a relatively high number of donor atoms as well as variation in their position within the ligands, resulting in a large versatility of the likely coordination modes. The review, besides presenting the solution equilibrium results, also discusses the main factors, such as (N,N) versus (O,O) chelate; size of chelate; amino-N versus imidazole-N; primary versus secondary hydroxamic function; differences between hydrolytic ability of the metal ions studied; and hydrolysis of the coordinated peptide hydroxamic acids in their Pd(II) complexes, which all determine the coordination modes present in the complexes formed in measurable concentrations in these systems. The options for the quantitative evaluation of metal binding effectivity and selectivity of the various ligands and the comparison with each other by using solution equilibrium data are also discussed.
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12
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Zhang Y, Yu Z, Lei L, Song Y, Liu S, Cui J, Dong C, Ding J, Cheng X, Su Y, Ma X. Secreted PEDF modulates fibroblast collagen synthesis through M1 macrophage polarization under expanded condition. Biomed Pharmacother 2021; 142:111951. [PMID: 34333290 DOI: 10.1016/j.biopha.2021.111951] [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: 11/17/2020] [Revised: 07/08/2021] [Accepted: 07/15/2021] [Indexed: 11/19/2022] Open
Abstract
Tissue expansion is widely used to obtain new skin tissue for repairing defects in the clinical practice of plastic surgery. One major complication can be dermal thinning during expansion, which usually leads to skin rupture. Collagen synthesis can determine dermal thickness and can be influenced by macrophage polarization during expansion. The aim of the study was to test whether pigment epithelium-derived factor (PEDF) could be a modulator of collagen synthesis in fibroblasts by regulating macrophage polarization during skin expansion. Our results showed that PEDF mRNA expression was increased in expanded human and mouse epidermis. PEDF protein levels were elevated in the subcutaneous exudates of a rat skin expansion model. Increased PEDF mRNA expression was accompanied by dermal thinning during a three-week expansion protocol. Subcutaneous injection of PEDF in vivo further resulted in dermal thinning and cell number increase of M1 macrophage in the expanded skin. PEDF also promoted macrophage polarization in vitro to the M1 subtype under hypoxic conditions. PEDF did not influence collagen gene expression in fibroblasts directly, but attenuated collagen synthesis in a macrophage-mediated manner. Additionally, blockage of PEDF receptors on macrophages with inhibitors rescued collagen synthesis in fibroblasts. Our research demonstrated PEDF elevation in expanded skin leads to dermal thinning through M1 macrophage-mediated collagen synthesis inhibition in fibroblasts. Our results could form a basis for the development of novel strategies to improve skin integrity in expanded skin by using PEDF.
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Affiliation(s)
- Yu Zhang
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, No.127 Changle West Road, Xi'an, Shaanxi Province 710032, China
| | - Zhou Yu
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, No.127 Changle West Road, Xi'an, Shaanxi Province 710032, China
| | - Lei Lei
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, No.127 Changle West Road, Xi'an, Shaanxi Province 710032, China
| | - Yajuan Song
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, No.127 Changle West Road, Xi'an, Shaanxi Province 710032, China
| | - Shiqiang Liu
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, No.127 Changle West Road, Xi'an, Shaanxi Province 710032, China
| | - Jiangbo Cui
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, No.127 Changle West Road, Xi'an, Shaanxi Province 710032, China
| | - Chen Dong
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, No.127 Changle West Road, Xi'an, Shaanxi Province 710032, China
| | - Jianke Ding
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, No.127 Changle West Road, Xi'an, Shaanxi Province 710032, China
| | - Xiaoxi Cheng
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, No.127 Changle West Road, Xi'an, Shaanxi Province 710032, China
| | - Yingjun Su
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, No.127 Changle West Road, Xi'an, Shaanxi Province 710032, China.
| | - Xianjie Ma
- Department of Plastic and Reconstructive Surgery, Xijing Hospital, Fourth Military Medical University, No.127 Changle West Road, Xi'an, Shaanxi Province 710032, China.
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Zafar W, Sumrra SH, Chohan ZH. A review: Pharmacological aspects of metal based 1,2,4-triazole derived Schiff bases. Eur J Med Chem 2021; 222:113602. [PMID: 34139626 DOI: 10.1016/j.ejmech.2021.113602] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 05/06/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022]
Abstract
Clinical reports have highlighted the radical increase of antibiotic resistance. As a result, multidrug resistance has emerged as a serious threat to human health. Many organic compounds commonly used as drugs in the past, no longer have pure organic mode of action rather need bio-transformation or more activation. Bulk of research has shown that they need trace amount of metal ions incorporated within the chemistry of bioactive molecules for enhancement of their potentiality to fight aggressively against resistance. The deficiency of some metal ions can also be responsible for many diseases like growth retardation, pernicious anemia and heart diseases in infants. To overcome these problems, there is a need to introduce novel strategies which have new mechanism of action along with significant spectrum of biological activity, enhanced safety and efficacy. Bioinorganic compounds have played imperative role in developing the new strategy in the form of "Metal Based Drugs". In current years there have been momentous rise of interest in the application of metal based Schiff base compounds to treat various diseases which are difficult to be treated with conventional methodologies. The unique properties of metal chelates acting as an intermediate between conventional organic and inorganic compounds provided innovative opportunities in the field of pharmaceutical chemistry. In this review, we have exclusively focused on the search of metal based 1,2,4-triazole derived Schiff base compounds (synthesized, reported and reviewed in the past ten years) that possess various biological activities such as antifungal, antibacterial, antioxidant, antidiabetic, anthelmintic, anticancer, antiproliferative, cytotoxic and DNA-intercalation activity.
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Affiliation(s)
- Wardha Zafar
- Department of Chemistry, University of Gujrat, Gujrat, 50700, Pakistan
| | - Sajjad H Sumrra
- Department of Chemistry, University of Gujrat, Gujrat, 50700, Pakistan.
| | - Zahid H Chohan
- Department of Chemistry, Institute of Southern Punjab, Multan, Pakistan
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Benzodiazepines: Drugs with Chemical Skeletons Suitable for the Preparation of Metallacycles with Potential Pharmacological Activity. Molecules 2021; 26:molecules26092796. [PMID: 34068533 PMCID: PMC8125983 DOI: 10.3390/molecules26092796] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/02/2022] Open
Abstract
The synthesis of organometallic compounds with potential pharmacological activity has attracted the attention of many research groups, aiming to take advantage of aspects that the presence of the metal-carbon bond can bring to the design of new pharmaceutical drugs. In this context, we have gathered studies reported in the literature in which psychoactive benzodiazepine drugs were used as ligands in the preparation of organometallic and metal complexes and provide details on some of their biological effects. We also highlight that most commonly known benzodiazepine-based drugs display molecular features that allow the preparation of metallacycles via C-H activation. These organometallic compounds merit further attention regarding their potential biological effects, not only in terms of psychoactive drugs but also in the search for drug replacements, for example, for cancer treatments.
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16
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Stevanović NL, Aleksic I, Kljun J, Skaro Bogojevic S, Veselinovic A, Nikodinovic-Runic J, Turel I, Djuran MI, Glišić BĐ. Copper(II) and Zinc(II) Complexes with the Clinically Used Fluconazole: Comparison of Antifungal Activity and Therapeutic Potential. Pharmaceuticals (Basel) 2020; 14:24. [PMID: 33396681 PMCID: PMC7823955 DOI: 10.3390/ph14010024] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 01/18/2023] Open
Abstract
Copper(II) and zinc(II) complexes with clinically used antifungal drug fluconazole (fcz), {[CuCl2(fcz)2].5H2O}n, 1, and {[ZnCl2(fcz)2]·2C2H5OH}n, 2, were prepared and characterized by spectroscopic and crystallographic methods. The polymeric structure of the complexes comprises four fluconazole molecules monodentately coordinated via the triazole nitrogen and two chlorido ligands. With respect to fluconazole, complex 2 showed significantly higher antifungal activity against Candida krusei and Candida parapsilosis. All tested compounds reduced the total amount of ergosterol at subinhibitory concentrations, indicating that the mode of activity of fluconazole was retained within the complexes, which was corroborated via molecular docking with cytochrome P450 sterol 14α-demethylase (CYP51) as a target. Electrostatic, steric and internal energy interactions between the complexes and enzyme showed that 2 has higher binding potency to this target. Both complexes showed strong inhibition of C. albicans filamentation and biofilm formation at subinhibitory concentrations, with 2 being able to reduce the adherence of C. albicans to A549 cells in vitro. Complex 2 was able to reduce pyocyanin production in Pseudomonas aeruginosa between 10% and 25% and to inhibit its biofilm formation by 20% in comparison to the untreated control. These results suggest that complex 2 may be further examined in the mixed Candida-P. aeruginosa infections.
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Affiliation(s)
- Nevena Lj. Stevanović
- Department of Chemistry, Faculty of Science, University of Kragujevac, R. Domanovića 12, 34000 Kragujevac, Serbia;
| | - Ivana Aleksic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (I.A.); (S.S.B.)
| | - Jakob Kljun
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia;
| | - Sanja Skaro Bogojevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (I.A.); (S.S.B.)
| | - Aleksandar Veselinovic
- Department of Chemistry, Faculty of Medicine, University of Niš, Blvd. Dr Zorana Djindjica 81, 18108 Niš, Serbia;
| | - Jasmina Nikodinovic-Runic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia; (I.A.); (S.S.B.)
| | - Iztok Turel
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia;
| | - Miloš I. Djuran
- Department of Chemical and Biological Sciences, Serbian Academy of Sciences and Arts, Knez Mihailova 35, 11000 Belgrade, Serbia
| | - Biljana Đ. Glišić
- Department of Chemistry, Faculty of Science, University of Kragujevac, R. Domanovića 12, 34000 Kragujevac, Serbia;
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Non-hydroxamate inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR): A critical review and future perspective. Eur J Med Chem 2020; 213:113055. [PMID: 33303239 DOI: 10.1016/j.ejmech.2020.113055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 12/22/2022]
Abstract
1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) catalyzes the second step of the non-mevalonate (or MEP) pathway that functions in several organisms and plants for the synthesis of isoprenoids. DXR is essential for the survival of multiple pathogenic bacteria/parasites, including those that cause tuberculosis and malaria in humans. DXR function is inhibited by fosmidomycin (1), a natural product, which forms a chelate with the active site divalent metal (Mg2+/Mn2+) through its hydroxamate metal-binding group (MBG). Most of the potent DXR inhibitors are structurally similar to 1 and retain hydroxamate despite the unfavourable pharmacokinetic and toxicity profile of the latter. We provide our perspective on the lack of non-hydroxamate DXR inhibitors. We also highlight the fundamental flaws in the design of MBG in these molecules, primarily responsible for their failure to inhibit DXR. We also suggest that for designing next-generation non-hydroxamate DXR inhibitors, approaches followed for other metalloenzymes targets may be exploited.
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Pistón M, Suárez A, Bühl V, Tissot F, Silva J, Panizzolo L. Influence of cooking processes on Cu, Fe, Mn, Ni, and Zn levels in beef cuts. J Food Compost Anal 2020. [DOI: 10.1016/j.jfca.2020.103624] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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19
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Design and synthesis of multi-target directed 1,2,3-triazole-dimethylaminoacryloyl-chromenone derivatives with potential use in Alzheimer's disease. BMC Chem 2020; 14:64. [PMID: 33134975 PMCID: PMC7592376 DOI: 10.1186/s13065-020-00715-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/08/2020] [Indexed: 02/01/2023] Open
Abstract
To discover multifunctional agents for the treatment of Alzheimer's disease (AD), a new series of 1,2,3-triazole-chromenone derivatives were designed and synthesized based on the multi target-directed ligands approach. The in vitro biological activities included acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibition as well as anti-Aβ aggregation, neuroprotective effects, and metal-chelating properties. The results indicated a highly selective BuChE inhibitory activity with an IC50 value of 21.71 μM for compound 10h as the most potent compound. Besides, compound 10h could inhibit self-induced Aβ1–42 aggregation and AChE-induced Aβ aggregation with 32.6% and 29.4% inhibition values, respectively. The Lineweaver–Burk plot and molecular modeling study showed that compound 10h targeted both the catalytic active site (CAS) and peripheral anionic site (PAS) of BuChE. It should be noted that compound 10h was able to chelate biometals. Thus, the designed scaffold could be considered as multifunctional agents in AD drug discovery developments. ![]()
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Li G, Su Y, Yan YH, Peng JY, Dai QQ, Ning XL, Zhu CL, Fu C, McDonough MA, Schofield CJ, Huang C, Li GB. MeLAD: an integrated resource for metalloenzyme-ligand associations. Bioinformatics 2020; 36:904-909. [PMID: 31504189 DOI: 10.1093/bioinformatics/btz648] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/29/2019] [Accepted: 08/19/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Metalloenzymes are attractive targets for therapeutic intervention owing to their central roles in various biological processes and pathological situations. The fast-growing body of structural data on metalloenzyme-ligand interactions is facilitating efficient drug discovery targeting metalloenzymes. However, there remains a shortage of specific databases that can provide centralized, interconnected information exclusive to metalloenzyme-ligand associations. RESULTS We created a Metalloenzyme-Ligand Association Database (MeLAD), which is designed to provide curated structural data and information exclusive to metalloenzyme-ligand interactions, and more uniquely, present expanded associations that are represented by metal-binding pharmacophores (MBPs), metalloenzyme structural similarity (MeSIM) and ligand chemical similarity (LigSIM). MeLAD currently contains 6086 structurally resolved interactions of 1416 metalloenzymes with 3564 ligands, of which classical metal-binding, non-classical metal-binding, non-metal-binding and metal water-bridging interactions account for 63.0%, 2.3%, 34.4% and 0.3%, respectively. A total of 263 monodentate, 191 bidentate and 15 tridentate MBP chemotypes were included in MeLAD, which are linked to different active site metal ions and coordination modes. 3726 and 52 740 deductive metalloenzyme-ligand associations by MeSIM and LigSIM analyses, respectively, were included in MeLAD. An online server is provided for users to conduct metalloenzyme profiling prediction for small molecules of interest. MeLAD is searchable by multiple criteria, e.g. metalloenzyme name, ligand identifier, functional class, bioinorganic class, metal ion and metal-containing cofactor, which will serve as a valuable, integrative data source to foster metalloenzyme related research, particularly involved in drug discovery targeting metalloenzymes. AVAILABILITY AND IMPLEMENTATION MeLAD is accessible at https://melad.ddtmlab.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gen Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yu Su
- College of Cybersecurity, Sichuan University, Chengdu, Sichuan 610065, China
| | - Yu-Hang Yan
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jia-Yi Peng
- College of Cybersecurity, Sichuan University, Chengdu, Sichuan 610065, China
| | - Qing-Qing Dai
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiang-Li Ning
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Cheng-Long Zhu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chen Fu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
| | | | | | - Cheng Huang
- College of Cybersecurity, Sichuan University, Chengdu, Sichuan 610065, China
| | - Guo-Bo Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, China
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Lisnyansky M, Yariv E, Segal O, Marom M, Loewenstein A, Ben-Tal N, Giladi M, Haitin Y. Metal Coordination Is Crucial for Geranylgeranyl Diphosphate Synthase–Bisphosphonate Interactions: A Crystallographic and Computational Analysis. Mol Pharmacol 2019; 96:580-588. [DOI: 10.1124/mol.119.117499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022] Open
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Sales TA, Prandi IG, Castro AAD, Leal DHS, Cunha EFFD, Kuca K, Ramalho TC. Recent Developments in Metal-Based Drugs and Chelating Agents for Neurodegenerative Diseases Treatments. Int J Mol Sci 2019; 20:E1829. [PMID: 31013856 PMCID: PMC6514778 DOI: 10.3390/ijms20081829] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/07/2019] [Accepted: 04/09/2019] [Indexed: 02/07/2023] Open
Abstract
The brain has a unique biological complexity and is responsible for important functions in the human body, such as the command of cognitive and motor functions. Disruptive disorders that affect this organ, e.g. neurodegenerative diseases (NDDs), can lead to permanent damage, impairing the patients' quality of life and even causing death. In spite of their clinical diversity, these NDDs share common characteristics, such as the accumulation of specific proteins in the cells, the compromise of the metal ion homeostasis in the brain, among others. Despite considerable advances in understanding the mechanisms of these diseases and advances in the development of treatments, these disorders remain uncured. Considering the diversity of mechanisms that act in NDDs, a wide range of compounds have been developed to act by different means. Thus, promising compounds with contrasting properties, such as chelating agents and metal-based drugs have been proposed to act on different molecular targets as well as to contribute to the same goal, which is the treatment of NDDs. This review seeks to discuss the different roles and recent developments of metal-based drugs, such as metal complexes and metal chelating agents as a proposal for the treatment of NDDs.
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Affiliation(s)
- Thais A Sales
- Laboratory of Molecular Modeling, Department of Chemistry, Federal University of Lavras, Lavras/MG, 37200-000, Brazil.
| | - Ingrid G Prandi
- Laboratory of Molecular Modeling, Department of Chemistry, Federal University of Lavras, Lavras/MG, 37200-000, Brazil.
| | - Alexandre A de Castro
- Laboratory of Molecular Modeling, Department of Chemistry, Federal University of Lavras, Lavras/MG, 37200-000, Brazil.
| | - Daniel H S Leal
- Department of Health Sciences, Federal University of Espírito Santo, São Mateus/ES, 29932-540, Brazil.
| | - Elaine F F da Cunha
- Laboratory of Molecular Modeling, Department of Chemistry, Federal University of Lavras, Lavras/MG, 37200-000, Brazil.
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, 500 03, Czech Republic..
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, 500 03 Czech Republic.
| | - Teodorico C Ramalho
- Laboratory of Molecular Modeling, Department of Chemistry, Federal University of Lavras, Lavras/MG, 37200-000, Brazil.
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, 500 03, Czech Republic..
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