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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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Yang H, Huang Z, Lehnherr D, Lam YH, Ren S, Strotman NA. Efficient Aliphatic Hydrogen-Isotope Exchange with Tritium Gas through the Merger of Photoredox and Hydrogenation Catalysts. J Am Chem Soc 2022; 144:5010-5022. [PMID: 35263094 DOI: 10.1021/jacs.1c13265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Employment of a combination of an organophotoredox catalyst with Wilkinson's catalyst (Rh(PPh3)3Cl) has given rise to an unprecedented method for hydrogen-isotope exchange (HIE) of aliphatic C(sp3)-H bonds of complex pharmaceuticals using T2 gas directly. Wilkinson's catalyst, commonly used for catalytic hydrogenations, was exploited as a precatalyst for activation of D2 or T2 and hydrogen atom transfer. In this combined methodology and mechanistic study, we demonstrate that by coupling photocatalysis with Rh catalysis, carbon-centered radicals generated via photoredox catalysis can be intercepted by Rh-hydride intermediates to deliver an effective hydrogen atom donor for hydrogen-isotope labeling of complex molecules in one step. By optimizing the ratio of the photocatalyst and Wilkinson's catalyst to balance the rate of the dual catalytic cycles, we can achieve efficient HIE and high recovery yield. This protocol was readily applied to direct HIE of C(sp3)-H bonds in 10 complex drug molecules, showing high isotope incorporation efficiency and exceptionally good functional group tolerance and demonstrating this approach as a practical and attractive labeling method for deuteration and tritiation.
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Affiliation(s)
- Haifeng Yang
- Process Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Zheng Huang
- Process Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Dan Lehnherr
- Process Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yu-Hong Lam
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Sumei Ren
- Process Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Neil A Strotman
- Process Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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Cheng J, Li X. Development and Application of Activity-based Fluorescent Probes for High-Throughput Screening. Curr Med Chem 2021; 29:1739-1756. [PMID: 34036907 DOI: 10.2174/0929867328666210525141728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 11/22/2022]
Abstract
High-throughput screening facilitates the rapid identification of novel hit compounds; however, it remains challenging to design effective high-throughput assays, partially due to the difficulty of achieving sensitivity in the assay techniques. Among the various analytical methods that are used, fluorescence-based assays dominate owing to their high sensitivity and ease of operation. Recent advances in activity-based sensing/imaging have further expanded the availability of fluorescent probes as monitors for high-throughput screening of result outputs. In this study, we have reviewed various activity-based fluorescent probes used in high-throughput screening assays, emphasizing their structure-related working mechanisms. Moreover, we have explored the possibility of the development of additional and better probes to boost hit identification and drug development against various targets.
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Affiliation(s)
- Juan Cheng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xin Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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Loh YY, Nagao K, Hoover AJ, Hesk D, Rivera NR, Colletti SL, Davies IW, MacMillan DWC. Photoredox-catalyzed deuteration and tritiation of pharmaceutical compounds. Science 2017; 358:1182-1187. [PMID: 29123019 PMCID: PMC5907472 DOI: 10.1126/science.aap9674] [Citation(s) in RCA: 330] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/30/2017] [Indexed: 12/24/2022]
Abstract
Deuterium- and tritium-labeled pharmaceutical compounds are pivotal diagnostic tools in drug discovery research, providing vital information about the biological fate of drugs and drug metabolites. Herein we demonstrate that a photoredox-mediated hydrogen atom transfer protocol can efficiently and selectively install deuterium (D) and tritium (T) at α-amino sp3 carbon-hydrogen bonds in a single step, using isotopically labeled water (D2O or T2O) as the source of hydrogen isotope. In this context, we also report a convenient synthesis of T2O from T2, providing access to high-specific-activity T2O. This protocol has been successfully applied to the high incorporation of deuterium and tritium in 18 drug molecules, which meet the requirements for use in ligand-binding assays and absorption, distribution, metabolism, and excretion studies.
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Affiliation(s)
- Yong Yao Loh
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA
| | - Kazunori Nagao
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA
| | - Andrew J Hoover
- Labeled Compound Synthesis Group, Department of Process R&D, Merck Research Laboratories (MRL), Merck & Co., Inc., Rahway, NJ 07065, USA
| | - David Hesk
- Labeled Compound Synthesis Group, Department of Process R&D, Merck Research Laboratories (MRL), Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Nelo R Rivera
- Labeled Compound Synthesis Group, Department of Process R&D, Merck Research Laboratories (MRL), Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Steven L Colletti
- Department of Discovery Chemistry, MRL, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Ian W Davies
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA
- Labeled Compound Synthesis Group, Department of Process R&D, Merck Research Laboratories (MRL), Merck & Co., Inc., Rahway, NJ 07065, USA
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA.
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