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Cui J, Feng Y, Yang T, Wang X, Tang H. Computer-Aided Designing Peptide Inhibitors of Human Hematopoietic Prostaglandin D2 Synthase Combined Molecular Docking and Molecular Dynamics Simulation. Molecules 2023; 28:5933. [PMID: 37570903 PMCID: PMC10421073 DOI: 10.3390/molecules28155933] [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: 07/17/2023] [Revised: 07/29/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Human hematopoietic prostaglandin D2 synthase (HPGDS) is involved in the production of prostaglandin D2, which participates in various physiological processes, including inflammation, allergic reactions, and sleep regulation. Inhibitors of HPGDS have been investigated as potential anti-inflammatory agents. For the investigation of potent HPGDS inhibitors, we carried out a computational modeling study combining molecular docking and molecular dynamics simulation for selecting and virtual confirming the designed binders. We selected the structure of HPGDS (PDB ID: 2CVD) carrying its native inhibitor compound HQL as our research target. The random 5-mer peptide library was created by building the 3-D structure of random peptides using Rosetta Buildpeptide and performing conformational optimization. Molecular docking was carried out by accommodating the peptides into the location of their native binder and then conducting docking using FlexPepDock. The two peptides RMYYY and VMYMI, which display the lowest binding energy against HPGDS, were selected to perform a comparative study. The interaction of RMYYY and VMYMI against HPGDS was further confirmed using molecular dynamics simulation and aligned with its native binder, HQL. We show the selected binders to have stronger binding energy and more frequent interactions against HPGDS than HQL. In addition, we analyzed the solubility, hydrophobicity, charge, and bioactivity of the generated peptides, and we show that the selected strong binder may be further used as therapeutic drugs.
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Affiliation(s)
- Jing Cui
- Wuxi Food Safety Inspection and Test Center, 35-210 South Changjiang Road, Wuxi 214142, China (T.Y.)
- Technology Innovation Center of Special Food for State Market Regulation, 35-302 South Changjiang Road, Wuxi 214142, China
| | - Yongwei Feng
- Wuxi Food Safety Inspection and Test Center, 35-210 South Changjiang Road, Wuxi 214142, China (T.Y.)
- Technology Innovation Center of Special Food for State Market Regulation, 35-302 South Changjiang Road, Wuxi 214142, China
| | - Ting Yang
- Wuxi Food Safety Inspection and Test Center, 35-210 South Changjiang Road, Wuxi 214142, China (T.Y.)
- Technology Innovation Center of Special Food for State Market Regulation, 35-302 South Changjiang Road, Wuxi 214142, China
| | - Xinglong Wang
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China;
| | - Heng Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, China
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Komkov AV, Sukhanova AА, Menchikov LG, Zavarzin IV. о-Aminopyrimidine Aldehydes and Ketones: Synthesis and use as Precursors to Fused Pyrimidines. Chem Heterocycl Compd (N Y) 2022. [DOI: 10.1007/s10593-022-03141-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Cossy J, Polàk P, Ruer PC. Incorporation of a cyclobutyl substituent in molecules by transition metal-catalyzed cross-coupling reactions. Org Biomol Chem 2022; 20:7529-7553. [PMID: 36148586 DOI: 10.1039/d2ob01045c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this review, the incorporation of a cyclobutyl substituent in molecules, by transition metal-catalyzed cross-coupling, is described by only considering the formation of C-C bonds. Three main strategies are used to introduce a cyclobutyl substituent in molecules by involving either electrophilic or nucleophilic cyclobutane derivatives.
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Affiliation(s)
- Janine Cossy
- Molecular, Macromolecular chemistry and Materials (C3M), ESPCI Paris, PSL, 10 rue Vauquelin, 75005 Paris, France.
| | - Peter Polàk
- Molecular, Macromolecular chemistry and Materials (C3M), ESPCI Paris, PSL, 10 rue Vauquelin, 75005 Paris, France.
| | - Paul C Ruer
- Molecular, Macromolecular chemistry and Materials (C3M), ESPCI Paris, PSL, 10 rue Vauquelin, 75005 Paris, France.
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Olson KL, Holt MC, Ciske FL, Kramer JB, Heiple PE, Collins ML, Johnson CM, Ho CS, Morano MI, Barrett SD. Novel amide and imidazole compounds as potent hematopoietic prostaglandin D 2 synthase inhibitors. Bioorg Med Chem Lett 2021; 34:127759. [PMID: 33383152 DOI: 10.1016/j.bmcl.2020.127759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/17/2020] [Accepted: 12/20/2020] [Indexed: 11/24/2022]
Abstract
In seeking novel and potent small molecule hematopoietic prostaglandin D2 synthase (H-PGDS) inhibitors as potential therapies for PGD2-mediated diseases and conditions, we explored a series comprising multiple aryl/heteroaryl rings attached in a linear arrangement. Each compound incorporates an amide or imidazole "linker" between the pyrimidine or pyridine "core" ring and the "tail" ring system. We synthesized and screened twenty analogs by fluorescence polarization binding assay, thermal shift assay, glutathione S-transferase inhibition assay, and a cell-based assay measuring suppression of LPS-induced PGD2 stimulation. Amide analogs show ten-fold greater shift in the thermal shift assay in the presence of glutathione (GSH) versus the same assay run in the absence of GSH. The imidazole analogs did not produce a significant change in thermal shift between the two assay conditions, suggesting a possible stabilization effect of the amide linker in the synthase-GSH-inhibitor complex. Imidazole analog 23, (KMN-010034) demonstrates superior potency across the in vitro assays and good in vitro metabolic stability in both human and guinea pig liver microsomes.
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Affiliation(s)
- Kirk L Olson
- Cayman Chemical Company, Inc., 1180 East Ellsworth Rd., Ann Arbor, MI, USA.
| | - Melissa C Holt
- Cayman Chemical Company, Inc., 1180 East Ellsworth Rd., Ann Arbor, MI, USA
| | - Fred L Ciske
- Cayman Chemical Company, Inc., 1180 East Ellsworth Rd., Ann Arbor, MI, USA
| | - James B Kramer
- Cayman Chemical Company, Inc., 1180 East Ellsworth Rd., Ann Arbor, MI, USA
| | - Paige E Heiple
- Cayman Chemical Company, Inc., 1180 East Ellsworth Rd., Ann Arbor, MI, USA
| | - Margaret L Collins
- Cayman Chemical Company, Inc., 1180 East Ellsworth Rd., Ann Arbor, MI, USA
| | - Carrie M Johnson
- Cayman Chemical Company, Inc., 1180 East Ellsworth Rd., Ann Arbor, MI, USA
| | - Chi S Ho
- Cayman Chemical Company, Inc., 1180 East Ellsworth Rd., Ann Arbor, MI, USA
| | - M Ines Morano
- Cayman Chemical Company, Inc., 1180 East Ellsworth Rd., Ann Arbor, MI, USA
| | - Stephen D Barrett
- Cayman Chemical Company, Inc., 1180 East Ellsworth Rd., Ann Arbor, MI, USA
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