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Sanina NA, Utenyshev AN, Dorovatovskii PV, Emel'yanova NS, Ovanesyan NS, Kulikov AV, Sulimenkov IV, Luzhkov VB, Pokidova OV, Aldoshin SM. Synthesis of a tetranitrosyl iron complex with unique structure and properties as an inhibitor of phosphodiesterases. Dalton Trans 2023; 52:18090-18101. [PMID: 37997167 DOI: 10.1039/d3dt03104g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
A novel neutral tetranitrosyl iron complex {[Fe(H2O)4]2+[FeR2(NO)2]22-}·4H2O (1) with R = 5-(3-pyridyl)-4H-1,2,4-triazole-3-thiolyls (C7H5N4S), which is a supramolecular ensemble, has been synthesized and studied. As follows from X-ray diffraction analysis, this is an octahedral Fe2+complex (Lewis acid) with two monoanionic dinitrosyl groups [FeR2(NO)2]- (Lewis base) and 4 water molecules as the ligands. As follows from Mössbauer spectra, the coordinating Fe2+ ion is in a low-spin state S = 0, and the dinitrosyl Fe+ ion is in a low-spin state S = 1/2. According to the data of EPR spectroscopy, mass-spectrometry and amperometry, complex 1 in solution forms dinitrosyl particles of [Fe(C7H6N4S-H)2(NO)2]- composition, which are responsible for NO generation. In addition, complex 1 was shown to be a 5-6 times more efficient phosphodiesterase (PDE) inhibitor at 5 × 10-5 M and 10-4 M concentrations than its thioligand. Probable binding sites of the [FeR2(NO)2]- ligand for the bovine PDE1B model have been determined by molecular docking and quantum-chemical calculations.
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Affiliation(s)
- N A Sanina
- Federal Research Center of Problems of Chemical Physics and Medicine Chemistry, Russian Academy of Sciences, 1 Acad. Semenov Av., Chernogolovka, 142432, Russia.
- M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
- Federal State University of Education, 141014, Mytishchi, Russia
| | - A N Utenyshev
- Federal Research Center of Problems of Chemical Physics and Medicine Chemistry, Russian Academy of Sciences, 1 Acad. Semenov Av., Chernogolovka, 142432, Russia.
| | - P V Dorovatovskii
- National Research Center "Kurchatov Institute", 123182, Moscow, Russia
| | - N S Emel'yanova
- Federal Research Center of Problems of Chemical Physics and Medicine Chemistry, Russian Academy of Sciences, 1 Acad. Semenov Av., Chernogolovka, 142432, Russia.
| | - N S Ovanesyan
- Federal Research Center of Problems of Chemical Physics and Medicine Chemistry, Russian Academy of Sciences, 1 Acad. Semenov Av., Chernogolovka, 142432, Russia.
| | - A V Kulikov
- Federal Research Center of Problems of Chemical Physics and Medicine Chemistry, Russian Academy of Sciences, 1 Acad. Semenov Av., Chernogolovka, 142432, Russia.
| | - I V Sulimenkov
- Chernogolovka Branch of N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Academician Semenov avenue 1/10, Chernogolovka, 142432, Moscow region, Russia
| | - V B Luzhkov
- Federal Research Center of Problems of Chemical Physics and Medicine Chemistry, Russian Academy of Sciences, 1 Acad. Semenov Av., Chernogolovka, 142432, Russia.
| | - O V Pokidova
- Federal Research Center of Problems of Chemical Physics and Medicine Chemistry, Russian Academy of Sciences, 1 Acad. Semenov Av., Chernogolovka, 142432, Russia.
| | - S M Aldoshin
- Federal Research Center of Problems of Chemical Physics and Medicine Chemistry, Russian Academy of Sciences, 1 Acad. Semenov Av., Chernogolovka, 142432, Russia.
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Niu Z, Lei P, Wang Y, Wang J, Yang J, Zhang J. Small molecule LpxC inhibitors against gram-negative bacteria: Advances and future perspectives. Eur J Med Chem 2023; 253:115326. [PMID: 37023679 DOI: 10.1016/j.ejmech.2023.115326] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/18/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Uridine diphosphate-3-O-(hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a metalloenzyme with zinc ions as cofactors and is a key enzyme in the essential structural outer membrane lipid A synthesis commitment step of gram-negative bacteria. As LpxC is extremely homologous among different Gram-negative bacteria, it is conserved in almost all gram-negative bacteria, which makes LpxC a promising target. LpxC inhibitors have been reported extensively in recent years, such as PF-5081090 and CHIR-090 were found to have broad-spectrum antibiotic activity against P. aeruginosa and E. coli. They are mainly classified into hydroxamate inhibitors and non-hydroxamate inhibitors based on their structure, but no LpxC inhibitors have been marketed due to safety and activity issues. This review, therefore, focuses on small molecule inhibitors of LpxC against gram-negative pathogenic bacteria and covers recent advances in LpxC inhibitors, focusing on their structural optimization process, structure-activity relationships, and future directions, with the aim of providing ideas for the development of LpxC inhibitors and clinical research.
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Ahmad S, Navid A, Akhtar AS, Azam SS, Wadood A, Pérez-Sánchez H. Subtractive Genomics, Molecular Docking and Molecular Dynamics Simulation Revealed LpxC as a Potential Drug Target Against Multi-Drug Resistant Klebsiella pneumoniae. Interdiscip Sci 2018; 11:508-526. [PMID: 29721784 DOI: 10.1007/s12539-018-0299-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/11/2018] [Accepted: 04/24/2018] [Indexed: 12/17/2022]
Abstract
The emergence and dissemination of pan drug resistant clones of Klebsiella pneumoniae are great threat to public health. In this regard new therapeutic targets must be highlighted to pave the path for novel drug discovery and development. Subtractive proteomic pipeline brought forth UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC), a Zn+2 dependent cytoplasmic metalloprotein and catalyze the rate limiting deacetylation step of lipid A biosynthesis pathway. Primary sequence analysis followed by 3-dimensional (3-D) structure elucidation of the protein led to the detection of K. pneumoniae LpxC (KpLpxC) topology distinct from its orthologous counterparts in other bacterial species. Molecular docking study of the protein recognized receptor antagonist compound 106, a uridine-based LpxC inhibitory compound, as a ligand best able to fit the binding pocket with a Gold Score of 67.53. Molecular dynamics simulation of docked KpLpxC revealed an alternate binding pattern of ligand in the active site. The ligand tail exhibited preferred binding to the domain I residues as opposed to the substrate binding hydrophobic channel of subdomain II, usually targeted by inhibitory compounds. Comparison with the undocked KpLpxC system demonstrated ligand induced high conformational changes in the hydrophobic channel of subdomain II in KpLpxC. Hence, ligand exerted its inhibitory potential by rendering the channel unstable for substrate binding.
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Affiliation(s)
- Sajjad Ahmad
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Afifa Navid
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Amina Saleem Akhtar
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Sikander Azam
- National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University-Mardan, Shankar Campus, Mardan, Khyber Pukhtoonkhwa, Pakistan
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica San Antonio de Murcia (UCAM), Murcia, Spain
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Li YS, Tian H, Zhao DS, Hu DK, Liu XY, Jin HW, Song GP, Cui ZN. Synthesis and bioactivity of pyrazole and triazole derivatives as potential PDE4 inhibitors. Bioorg Med Chem Lett 2016; 26:3632-5. [DOI: 10.1016/j.bmcl.2016.06.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/18/2016] [Accepted: 06/02/2016] [Indexed: 11/30/2022]
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Pérez-Garrido A, Helguera AM, Rodríguez FG, Cordeiro MNDS. QSAR models to predict mutagenicity of acrylates, methacrylates and alpha,beta-unsaturated carbonyl compounds. Dent Mater 2010; 26:397-415. [PMID: 20122717 DOI: 10.1016/j.dental.2009.11.158] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2009] [Revised: 09/08/2009] [Accepted: 11/26/2009] [Indexed: 11/17/2022]
Abstract
OBJECTIVE The purpose of this study is to develop a quantitative structure-activity relationship (QSAR) model that can distinguish mutagenic from non-mutagenic species with alpha,beta-unsaturated carbonyl moiety using two endpoints for this activity - Ames test and mammalian cell gene mutation test - and also to gather information about the molecular features that most contribute to eliminate the mutagenic effects of these chemicals. METHODS Two data sets were used for modeling the two mutagenicity endpoints: (1) Ames test and (2) mammalian cells mutagenesis. The first one comprised 220 molecules, while the second one 48 substances, ranging from acrylates, methacrylates to alpha,beta-unsaturated carbonyl compounds. The QSAR models were developed by applying linear discriminant analysis (LDA) along with different sets of descriptors computed using the DRAGON software. RESULTS For both endpoints, there was a concordance of 89% in the prediction and 97% confidentiality by combining the three models for the Ames test mutagenicity. We have also identified several structural alerts to assist the design of new monomers. SIGNIFICANCE These individual models and especially their combination are attractive from the point of view of molecular modeling and could be used for the prediction and design of new monomers that do not pose a human health risk.
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Affiliation(s)
- Alfonso Pérez-Garrido
- Enviromental Engineering and Toxicology Dpt., Catholic University of San Antonio, Guadalupe, Murcia, Spain.
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Kadam RU, Chavan AG, Monga V, Kaur N, Jain R, Roy N. Selectivity-based QSAR approach for screening and evaluation of TRH analogs for TRH-R1 and TRH-R2 receptors subtypes. J Mol Graph Model 2008; 27:309-20. [PMID: 18595758 DOI: 10.1016/j.jmgm.2008.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 05/20/2008] [Accepted: 05/20/2008] [Indexed: 11/28/2022]
Abstract
Design and development of therapeutically useful CNS selective thyrotropin-releasing hormone (TRH) analogs acting on TRH-R2 receptor subtype, exerting weak or no TRH-R1-mediated TSH-releasing side effects has gained imagination of researchers in the recent past. The present study reports the development and implementation of a selectivity-based QSAR approach for screening selective agonists of TRH-R2 receptor subtype. The statistically significant predictive models were thoroughly validated using an external validation set whose activity was previously unknown. The model was able to predict preference for either of the receptor subtypes successfully.
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Affiliation(s)
- Rameshwar U Kadam
- Centre of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar 160062, Punjab, India
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Kadam RU, Garg D, Roy N. Selective Mapping of Chemical Space for Pseudomonas aeruginosa Deacetylase LpxC Inhibitory Potential. Chem Biol Drug Des 2007; 71:45-56. [DOI: 10.1111/j.1747-0285.2007.00608.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Kadam RU, Garg D, Paul AT, Bhutani KK, Roy N. Evaluation of Proinflammatory Cytokine Pathway Inhibitors for p38 MAPK Inhibitory Potential. J Med Chem 2007; 50:6337-42. [DOI: 10.1021/jm0706923] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Rameshwar U. Kadam
- Centre of Pharmacoinformatics and Department of Natural Products, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar-160 062, Punjab, India
| | - Divita Garg
- Centre of Pharmacoinformatics and Department of Natural Products, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar-160 062, Punjab, India
| | - Atish T. Paul
- Centre of Pharmacoinformatics and Department of Natural Products, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar-160 062, Punjab, India
| | - K. K. Bhutani
- Centre of Pharmacoinformatics and Department of Natural Products, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar-160 062, Punjab, India
| | - Nilanjan Roy
- Centre of Pharmacoinformatics and Department of Natural Products, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S Nagar-160 062, Punjab, India
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Density gradient enrichment of Escherichia coli conditional msbA mutants. Appl Environ Microbiol 2007; 73:7992-6. [PMID: 17965211 DOI: 10.1128/aem.01992-07] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Insight into the mechanism of lipid transport to the outer membrane of gram-negative bacteria has been hampered by the lack of an effective genetic screen for defective mutants. This work demonstrates an enrichment of conditional mutants defective in lipopolysaccharide export by Ludox density gradient centrifugation and selection for detergent resistance. New temperature-sensitive mutants with lipid export defects were isolated with single missense mutations in msbA. The results demonstrate the power of this approach for the study of lipid export in Escherichia coli.
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