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Chan AHY, Ho TCS, Irfan R, Hamid RAA, Rudge ES, Iqbal A, Turner A, Hirsch AKH, Leeper FJ. Design of thiamine analogues for inhibition of thiamine diphosphate (ThDP)-dependent enzymes: Systematic investigation through Scaffold-Hopping and C2-Functionalisation. Bioorg Chem 2023; 138:106602. [PMID: 37201323 DOI: 10.1016/j.bioorg.2023.106602] [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: 03/17/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023]
Abstract
Thiamine diphosphate (ThDP), the bioactive form of vitamin B1, is an essential coenzyme needed for processes of cellular metabolism in all organisms. ThDP-dependent enzymes all require ThDP as a coenzyme for catalytic activity, although individual enzymes vary significantly in substrate preferences and biochemical reactions. A popular way to study the role of these enzymes through chemical inhibition is to use thiamine/ThDP analogues, which typically feature a neutral aromatic ring in place of the positively charged thiazolium ring of ThDP. While ThDP analogues have aided work in understanding the structural and mechanistic aspects of the enzyme family, at least two key questions regarding the ligand design strategy remain unresolved: 1) which is the best aromatic ring? and 2) how can we achieve selectivity towards a given ThDP-dependent enzyme? In this work, we synthesise derivatives of these analogues covering all central aromatic rings used in the past decade and make a head-to-head comparison of all the compounds as inhibitors of several ThDP-dependent enzymes. Thus, we establish the relationship between the nature of the central ring and the inhibitory profile of these ThDP-competitive enzyme inhibitors. We also demonstrate that introducing a C2-substituent onto the central ring to explore the unique substrate-binding pocket can further improve both potency and selectivity.
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Affiliation(s)
- Alex H Y Chan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Terence C S Ho
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Rimsha Irfan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Rawia A A Hamid
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Emma S Rudge
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Amjid Iqbal
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Biochemistry, Science Unit, Deanship of Educational Services, Qassim University, Saudi Arabia
| | - Alex Turner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Finian J Leeper
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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Sukanya R, Aruldhas D, HubertJoe I, Balachandran S. Synthesis, Spectroscopic (FTIR, FT-Raman and UV-Vis), Structural Investigation, Chemical Reactivity, AIM, NBO, NLO, Hirshfeld Analysis of 4-Aminobenzoic Acid Pyrazinoic Acid. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2165513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- R. Sukanya
- Manonmanium Sundaranar University, Tirunelveli, Tamil Nadu, India
- Department of Physics & Research Centre, Nesamony Memmorial Christian College, Marthandam, Tamil Nadu, India
| | - D. Aruldhas
- Department of Physics & Research Centre, Nesamony Memmorial Christian College, Marthandam, Tamil Nadu, India
| | - I. HubertJoe
- Kerala University, Thiruvanthapuram, Kerala, India
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Şahin S, Dege N. (E)-N-(3-chlorophenyl)-1-(5-nitro-2-(piperidin-1-yl)phenyl)methanimine: X-Ray, DFT, ADMET, Boiled-Egg Model, Druggability, Bioavailabilty, and Human Cyclophilin D (CypD) Inhibitory Activity. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131744] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Zhou Y, Cai M, Zhou H, Hou L, Peng H, He H. Discovery of efficient inhibitors against pyruvate dehydrogenase complex component E1 with bactericidal activity using computer aided design. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 177:104894. [PMID: 34301356 DOI: 10.1016/j.pestbp.2021.104894] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/15/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
Computer aided optimization of lead compounds is of great significance to the design and discovery of new agrochemicals. A series of 2,6-dimethyl-4-aminopyrimidine acylhydrazones 6 was rationally designed as pyruvate dehydrogenase complex component E1 (PDHc-E1) inhibitors using computer aided drug design. Compounds in series 6 showed excellent inhibitory activity against Escherichia coli PDHc-E1, which was considerably higher than that of the lead compound A2. Compound 6l showed the best inhibitory activity (IC50 = 95 nM). Molecular docking, site-directed mutagenesis, and enzymatic assays revealed that the compounds bound in a "straight" conformation in the active site of E. coli PDHc-E1. Compounds 6b, 6e, and 6l showed negligible inhibition against porcine PDHc-E1. The in vitro antibacterial activity indicated that 6a, 6d, 6e, 6g, 6h, 6i, 6m, and 6n exhibited 61%-94% inhibition against Ralstonia solanacearum at 100 μg/mL, which was better than commercial thiodiazole‑copper (29%) and bismerthiazol (55%). These results demonstrated that a lead structure for a highly selective PDHc-E1 inhibitor as a bactericide could be obtained using computer aided drug design.
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Affiliation(s)
- Yuan Zhou
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, PR China
| | - Meng Cai
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, PR China
| | - Huan Zhou
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, PR China
| | - Leifeng Hou
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, PR China
| | - Hao Peng
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, PR China
| | - Hongwu He
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, PR China.
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Şahin S, Dege N. A newly synthesized small molecule: the evaluation against Alzheimer's Disease by in silico drug design and computational structure analysis methods. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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