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Zhang Y, Yu X, Gao D, Chen L, Zhang Z, Liu Y, Zheng Z, Chen J, Li C, Meng Q. Macrocyclic Neutralizer to Polybrene via Direct Host-Guest Complexation. J Med Chem 2024; 67:10425-10435. [PMID: 38848302 DOI: 10.1021/acs.jmedchem.4c00871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Hexadimethrine bromide (HB), a synthetic polycationic species, was introduced to clinical practice as a heparin antidote and recently used in gene therapy. However, HB causes various complications such as severe red blood cells (RBCs) aggregation and tissue damage. Herein, we have synthesized a water-soluble quaterphen[3]arene containing multiple sulfonate moieties (SQP3) as a novel macrocyclic neutralizer to reverse HB via direct host-guest complexation. SQP3 exhibited a robust binding affinity toward HB with a considerably high association constant of (4.73 ± 0.61) × 107 M-1. Co-dosed with 1 equiv of SQP3, HB-induced RBCs aggregation and blood coagulation could be effectively reversed. In vitro cellular assay verified that complexation of HB with SQP3 significantly decreased reactive oxygen species production, thereby suppressing cell apoptosis. In vivo neutralization efficacy studies demonstrated that HB/SQP3 was capable of alleviating related organic damage caused by HB and improving the survival rate of HB-treated mice from 20 to 100%.
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Affiliation(s)
- Yahan Zhang
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Xiang Yu
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Di Gao
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Longming Chen
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Ziliang Zhang
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Yuanyuan Liu
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Zhibing Zheng
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Junyi Chen
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
- Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry, Ministry of Education, Tianjin Key Laboratory of Structure and Performance for Functional Molecules, College of Chemistry, Tianjin Normal University, Tianjin 300387, P. R. China
| | - Chunju Li
- Key Laboratory of Inorganic-Organic Hybrid Functional Material Chemistry, Ministry of Education, Tianjin Key Laboratory of Structure and Performance for Functional Molecules, College of Chemistry, Tianjin Normal University, Tianjin 300387, P. R. China
| | - Qingbin Meng
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
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2
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Huo M, Song SQ, Dai XY, Li FF, Hu YY, Liu Y. Phosphorescent acyclic cucurbituril solid supramolecular multicolour delayed fluorescence behaviour. Chem Sci 2024; 15:5163-5173. [PMID: 38577356 PMCID: PMC10988582 DOI: 10.1039/d4sc00160e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/26/2024] [Indexed: 04/06/2024] Open
Abstract
Organic photoluminescent macrocyclic hosts have been widely advanced in many fields. Phosphorescent hosts with the ability to bind organic guests have rarely been reported. Herein, acyclic cucurbituril modified with four carboxylic acids (ACB-COOH) is mined to present uncommon purely organic room-temperature phosphorescence (RTP) at 510 nm with a lifetime of 1.86 μs. Its RTP properties are significantly promoted with an extended lifetime up to 2.12 s and considerable quantum yield of 6.29% after assembly with a polyvinyl alcohol (PVA) matrix. By virtue of the intrinsic self-crimping configuration of ACB-COOH, organic guests, including fluorescence dyes (Rhodamine B (RhB) and Pyronin Y (PyY)) and a drug molecule (morphine (Mor)), could be fully encapsulated by ACB-COOH to attain energy transfer involving phosphorescent acyclic cucurbituril. Ultimately, as-prepared systems are successfully exploited to establish multicolor afterglow materials and visible sensing of morphine. As an expansion of phosphorescent acyclic cucurbituril, the host afterglow color can be readily regulated by attaching different aromatic sidewalls. This study develops the fabrication strategies and application scope of a supramolecular phosphorescent host and opens up a new direction for the manufacture of intelligent long-lived luminescent materials.
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Affiliation(s)
- Man Huo
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Shuang-Qi Song
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Xian-Yin Dai
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Fan-Fan Li
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Yu-Yang Hu
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Yu Liu
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University Tianjin 300071 P. R. China
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3
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Yin H, Cheng Q, Bardelang D, Wang R. Challenges and Opportunities of Functionalized Cucurbiturils for Biomedical Applications. JACS AU 2023; 3:2356-2377. [PMID: 37772183 PMCID: PMC10523374 DOI: 10.1021/jacsau.3c00273] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 09/30/2023]
Abstract
Cucurbit[n]uril (CB[n]) macrocycles (especially CB[5] to CB[8]) have shown exceptional attributes since their discovery in 2000. Their stability, water solubility, responsiveness to several stimuli, and remarkable binding properties have enabled a growing number of biological applications. Yet, soon after their discovery, the challenge of their functionalization was set. Nevertheless, after more than two decades, a myriad of CB[n] derivatives has been described, many of them used in cells or in vivo for advanced applications. This perspective summarizes key advances of this burgeoning field and points to the next opportunities and remaining challenges to fully express the potential of these fascinating macrocycles in biology and biomedical sciences.
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Affiliation(s)
- Hang Yin
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University
of Macau, Taipa, Macau 999078, China
| | - Qian Cheng
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University
of Macau, Taipa, Macau 999078, China
| | | | - Ruibing Wang
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University
of Macau, Taipa, Macau 999078, China
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4
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Brockett AT, Xue W, King D, Deng CL, Zhai C, Shuster M, Rastogi S, Briken V, Roesch MR, Isaacs L. Pillar[6]MaxQ: A Potent Supramolecular Host for In Vivo Sequestration of Methamphetamine and Fentanyl. Chem 2023; 9:881-900. [PMID: 37346394 PMCID: PMC10281757 DOI: 10.1016/j.chempr.2022.11.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pillar[6]MaxQ (P6AS) functions as an in vivo sequestration agent for methamphetamine and fentanyl. We use 1H NMR, isothermal titration calorimetry, and molecular modelling to deduce the geometry and strength of the P6AS•drug complexes. P6AS forms tight complexes with fentanyl (Kd=9.8 nM), PCP (17.1 nM), MDMA (25.5 nM), mephedrone (52.4 nM), and methamphetamine (101 nM). P6AS has good in vitro biocompatibility according to MTS metabolic, Adenylate Kinase cell death, and hERG ion channel inhibition assays, and the Ames fluctuation test. The no observed adverse effect level for P6AS is 45 mg/kg. The hyperlocomotion of mice treated with methamphetamine (0.5 mg/kg) can be ameliorated by treatment with P6AS (35.7 mg/kg) 5-minutes later, whereas the hyperlocomotion of mice treated with fentanyl (0.1 mg/kg) can be controlled by treatment with P6AS (5 mg/kg) up to 15-minutes later. P6AS has significant potential for development as a broad spectrum in vivo sequestration agent.
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Affiliation(s)
- Adam T. Brockett
- Department of Psychology and Program in Neuroscience and Cognitive Science (NACS), University of Maryland, College Park, MD 20742, United States
| | - Weijian Xue
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States
| | - David King
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States
| | - Chun-Lin Deng
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States
| | - Canjia Zhai
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States
| | - Michael Shuster
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, United States
| | - Shivangi Rastogi
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, United States
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, United States
| | - Matthew R. Roesch
- Department of Psychology and Program in Neuroscience and Cognitive Science (NACS), University of Maryland, College Park, MD 20742, United States
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States
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5
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Sun Z, He Q, Gong Z, Kalhor P, Huai Z, Liu Z. A General Picture of Cucurbit[8]uril Host–Guest Binding: Recalibrating Bonded Interactions. Molecules 2023; 28:molecules28073124. [PMID: 37049887 PMCID: PMC10095826 DOI: 10.3390/molecules28073124] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/15/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Atomic-level understanding of the dynamic feature of host–guest interactions remains a central challenge in supramolecular chemistry. The remarkable guest binding behavior of the Cucurbiturils family of supramolecular containers makes them promising drug carriers. Among Cucurbit[n]urils, Cucurbit[8]uril (CB8) has an intermediate portal size and cavity volume. It can exploit almost all host–guest recognition motifs formed by this host family. In our previous work, an extensive computational investigation of the binding of seven commonly abused and structurally diverse drugs to the CB8 host was performed, and a general dynamic binding picture of CB8-guest interactions was obtained. Further, two widely used fixed-charge models for drug-like molecules were investigated and compared in great detail, aiming at providing guidelines in choosing an appropriate charge scheme in host-guest modelling. Iterative refitting of atomic charges leads to improved binding thermodynamics and the best root-mean-squared deviation from the experimental reference is 2.6 kcal/mol. In this work, we focus on a thorough evaluation of the remaining parts of classical force fields, i.e., the bonded interactions. The widely used general Amber force fields are assessed and refitted with generalized force-matching to improve the intra-molecular conformational preference, and thus the description of inter-molecular host–guest interactions. The interaction pattern and binding thermodynamics show a significant dependence on the modelling parameters. The refitted system-specific parameter set improves the consistency of the modelling results and the experimental reference significantly. Finally, combining the previous charge-scheme comparison and the current force-field refitting, we provide general guidelines for the theoretical modelling of host–guest binding.
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6
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Sun JD, Liu Y, Zhao Z, Yu SB, Qi QY, Zhou W, Wang H, Hu K, Zhang DW, Li ZT. Host-guest binding of tetracationic cyclophanes to photodynamic agents inhibits posttreatment phototoxicity and maintains antitumour efficacy. RSC Med Chem 2023; 14:563-572. [PMID: 36970143 PMCID: PMC10034117 DOI: 10.1039/d2md00463a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
In the past two decades, photodynamic therapy (PDT) has become an effective method for the treatment of cancer. However, the posttreatment residue of photodynamic agents (PDAs) causes long-term skin phototoxicity. Here, we apply naphthalene-derived, box-like tetracationic cyclophanes, named NpBoxes, to bind to clinically used porphyrin-based PDAs to alleviate their posttreatment phototoxicity by reducing their free content in skin tissues and 1O2 quantum yield. We show that one of the cyclophanes, 2,6-NpBox, could include the PDAs to efficiently suppress their photosensitivity for the generation of reactive oxygen species. A tumour-bearing mouse model study revealed that, when Photofrin, the most widely used PDA in clinic, was administrated at a dose corresponding to the clinical one, 2,6-NpBox of the same dose could significantly suppress its posttreatment phototoxicity on the skin induced by simulated sunlight irradiation, without imposing a negative influence on its PDT efficacy.
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Affiliation(s)
- Jian-Da Sun
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University 2205 Songhu Road Shanghai 200438 China
| | - Yamin Liu
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University 2205 Songhu Road Shanghai 200438 China
| | - Zijian Zhao
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University 2205 Songhu Road Shanghai 200438 China
| | - Shang-Bo Yu
- Key Laboratory of Synthetic and Self-Assembly Chemistry for Organic Functional Molecules, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Lu Shanghai 200032 China
| | - Qiao-Yan Qi
- Key Laboratory of Synthetic and Self-Assembly Chemistry for Organic Functional Molecules, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Lu Shanghai 200032 China
| | - Wei Zhou
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University 2205 Songhu Road Shanghai 200438 China
| | - Hui Wang
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University 2205 Songhu Road Shanghai 200438 China
| | - Ke Hu
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University 2205 Songhu Road Shanghai 200438 China
| | - Dan-Wei Zhang
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University 2205 Songhu Road Shanghai 200438 China
| | - Zhan-Ting Li
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University 2205 Songhu Road Shanghai 200438 China
- Key Laboratory of Synthetic and Self-Assembly Chemistry for Organic Functional Molecules, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Lu Shanghai 200032 China
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7
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Amezcua M, Setiadi J, Ge Y, Mobley DL. An overview of the SAMPL8 host-guest binding challenge. J Comput Aided Mol Des 2022; 36:707-734. [PMID: 36229622 PMCID: PMC9596595 DOI: 10.1007/s10822-022-00462-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022]
Abstract
The SAMPL series of challenges aim to focus the community on specific modeling challenges, while testing and hopefully driving progress of computational methods to help guide pharmaceutical drug discovery. In this study, we report on the results of the SAMPL8 host–guest blind challenge for predicting absolute binding affinities. SAMPL8 focused on two host–guest datasets, one involving the cucurbituril CB8 (with a series of common drugs of abuse) and another involving two different Gibb deep-cavity cavitands. The latter dataset involved a previously featured deep cavity cavitand (TEMOA) as well as a new variant (TEETOA), both binding to a series of relatively rigid fragment-like guests. Challenge participants employed a reasonably wide variety of methods, though many of these were based on molecular simulations, and predictive accuracy was mixed. As in some previous SAMPL iterations (SAMPL6 and SAMPL7), we found that one approach to achieve greater accuracy was to apply empirical corrections to the binding free energy predictions, taking advantage of prior data on binding to these hosts. Another approach which performed well was a hybrid MD-based approach with reweighting to a force matched QM potential. In the cavitand challenge, an alchemical method using the AMOEBA-polarizable force field achieved the best success with RMSE less than 1 kcal/mol, while another alchemical approach (ATM/GAFF2-AM1BCC/TIP3P/HREM) had RMSE less than 1.75 kcal/mol. The work discussed here also highlights several important lessons; for example, retrospective studies of reference calculations demonstrate the sensitivity of predicted binding free energies to ethyl group sampling and/or guest starting pose, providing guidance to help improve future studies on these systems.
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Affiliation(s)
- Martin Amezcua
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Jeffry Setiadi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yunhui Ge
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA. .,Department of Chemistry, University of California, Irvine, CA, 92697, USA.
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8
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Wang L, Xu M, Zhou H, Yan K, Duan S, Xue D, Wang Y, Di B, Hu C. Teaching PCR for Simultaneous Sensing of Gene Transcription and Downstream Metabolites by Cucurbit[8]uril-Mediated Intervention of Polymerase Activity. Anal Chem 2022; 94:8715-8723. [PMID: 35671188 DOI: 10.1021/acs.analchem.2c01103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The target of typical PCR analysis is restricted to nucleic acids. To this end, we report here a novel strategy to simultaneously detect genetic and metabolic markers using commercial PCR kits with cucurbit[8]urils (CB[8]) implemented to manipulate the activity of Taq DNA polymerase. CB[8] binds with the nonionic surfactants and displaces them from the polymerase surface, resulting in decreased enzyme activity. Meanwhile, the inhibited enzyme can be reversibly activated when spermine, the downstream metabolite of ornithine decarboxylase (ODC), is present in the sample, which competitively binds to CB[8] and recovers polymerase activity. CB[8] was implemented in conventional PCR kits not only to reduce false-positive results but also to extend the detection range of PCR technology. With this novel method to detect ODC in cell lysates containing both the nucleotides and intracellular metabolites, positive results were only observed in highly active HEK 293T cells, whereas silent cells treated with ODC inhibitor showed negative readouts, therefore providing a simple but elegant dual-modality PCR method for precision diagnosis.
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Affiliation(s)
- Lancheng Wang
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Mingjie Xu
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Huimin Zhou
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Kun Yan
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Shiqi Duan
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Dandan Xue
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Youmei Wang
- Key Laboratory of Drug Monitoring and Control, Drug Intelligence and Forensic Center, Ministry of Public Security, No. 18 Dongbeiwang West Road, Beijing 100193, China
| | - Bin Di
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
| | - Chi Hu
- China National Narcotics Control Commission, China Pharmaceutical University, Joint Laboratory on Key Technologies of Narcotics Control, No. 24 Tongjiaxiang Road, Nanjing 210009, China
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9
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Zhu G, You A, Song H, Li Z. A combined crystallography and DFT study on ring-shaped Cucurbit[ n]urils: structures, surface character, and host-guest recognition. RSC Adv 2022; 12:10014-10019. [PMID: 35424911 PMCID: PMC8965660 DOI: 10.1039/d2ra00797e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/24/2022] [Indexed: 12/12/2022] Open
Abstract
A combined crystallography and DFT study of cucurbit[n]urils (n = 5-8, 10) was carried out, and PBE0 was certified to be the most rational density functional method for optimization task. Steric hindrance and electronic effect of the hindered lone pair electrons in cucurbit[n]urils were qualitatively measured by bond order analysis, lone pair electron (LP) visualization and electrostatic potential (ESP) study. Together with energy decomposition analysis of some selected host-guest systems, we quantitatively verified the effect of size/cavity and noncovalent interaction in host-guest recognition. This solid study revealed that lone pairs electrons affect not only on host-guest identification mode but also on geometry stability, which pave the avenue for further sophisticated applications.
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Affiliation(s)
- Guoxun Zhu
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou) Guangzhou 510070 P. R. China
| | - Ao You
- School of Eco-Environmental Technology, Guangdong Industry Polytechnic Guangzhou 510300 P. R. China
| | - Huacan Song
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou) Guangzhou 510070 P. R. China
- School of Chemical Engineering and Technology, Sun Yat-sen University Tangjia Zhuhai City 519082 P. R. China
| | - Zhengquan Li
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou) Guangzhou 510070 P. R. China
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10
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DiMaggio D, Brockett A, Shuster M, Murkli S, Zhai C, King D, O'Dowd B, Cheng M, Brady K, Briken V, Roesch MR, Isaacs L. Anthracene Walled Acyclic CB[n] Receptors: In Vitro and In Vivo Binding Properties Toward Drugs of Abuse. ChemMedChem 2022; 17:e202200046. [PMID: 35238177 DOI: 10.1002/cmdc.202200046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/01/2022] [Indexed: 11/07/2022]
Abstract
We report studies of the interaction of six acyclic CB[n]-type receptors toward a panel of drugs of abuse by a combination of isothermal titration calorimetry and 1H NMR spectroscopy. Anthracene walled acyclic CB[n] host (M3) displays highest binding affinity toward methamphetamine (Kd = 15 nM) and fentanyl (Kd = 4 nM). Host M3 is well tolerated by Hep G2 and HEK 293 cells up to 100 mM according to MTS metabolic and adenylate kinase release assays. An in vivomaximum tolerated dose study with Swiss Webster mice showed no adverse effects at the highest dose studied (44.7 mg kg-1). Host M3 is not mutagenic based on the Ames fluctuation test and does not inhibit the hERG ion channel. In vivoefficacy studies showed that pretreatment of mice with M3 significantly reduces the hyperlocomotion after treatment with methamphetamine, but M3 does not function similarly when administered 30 seconds after methamphetamine.
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Affiliation(s)
- Delaney DiMaggio
- University of Maryland at College Park, Chemistry and Biochemistry, 8051 Regents Dr., 20742, College Park, UNITED STATES
| | - Adam Brockett
- University of Maryland at College Park, Psychology, UNITED STATES
| | - Michael Shuster
- University of Maryland at College Park, Cell Biology and Molecular Genetics, UNITED STATES
| | - Steven Murkli
- University of Maryland at College Park, Chemistry and Biochemistry, UNITED STATES
| | - Canjia Zhai
- University of Maryland at College Park, Chemistry and Biochemistry, UNITED STATES
| | - David King
- University of Maryland at College Park, Chemistry and Biochemistry, UNITED STATES
| | - Brona O'Dowd
- University of Maryland at College Park, Chemistry and Biochemistry, UNITED STATES
| | - Ming Cheng
- University of Maryland at College Park, Chemistry and Biochemistry, UNITED STATES
| | - Kimberly Brady
- University of Maryland at College Park, Chemistry and Biochemistry, UNITED STATES
| | - Volker Briken
- University of Maryland at College Park, Cell Biology and Molecular Genetics, UNITED STATES
| | - Matthew R Roesch
- University of Maryland at College Park, Psychology, UNITED STATES
| | - Lyle Isaacs
- University of Maryland, College Park, Department of Chemistry and Biochemistry, Building 091, 20742, College Park, UNITED STATES
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11
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Deng CL, Cheng M, Zavalij PY, Isaacs L. Thermodynamics of Pillararene•Guest Complexation: Blinded Dataset for the SAMPL9 Challenge. NEW J CHEM 2022; 46:995-1002. [PMID: 35250257 PMCID: PMC8896905 DOI: 10.1039/d1nj05209h] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We report an investigation of the complexation between a water soluble pillararene host (WP6) and a panel of hydrophobic cationic guests (G1 - G20) by a combination of 1H NMR spectroscopy and isothermal titration calorimetry in phosphate buffered saline. We find that WP6 forms 1:1 complexes with Ka values in the 104 - 109 M-1 range driven by favorable enthalpic contributions. This thermodynamic dataset serves as blinded data for the SAMPL9 challenge.
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Affiliation(s)
- Chun-Lin Deng
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Ming Cheng
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Peter Y. Zavalij
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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12
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Markthaler D, Kraus H, Hansen N. Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange. J Comput Aided Mol Des 2022; 36:1-9. [PMID: 34978001 PMCID: PMC8831271 DOI: 10.1007/s10822-021-00439-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/11/2021] [Indexed: 11/20/2022]
Abstract
Umbrella sampling along a one-dimensional order parameter in combination with Hamiltonian replica exchange was employed to calculate the binding free energy of five guest molecules with known affinity to cucurbit[8]uril. A simple empirical approach correcting for the overestimation of the affinity by the GAFF force field was proposed and subsequently applied to the seven guest molecules of the “Drugs of Abuse” SAMPL8 challenge. Compared to the uncorrected binding free energies, the systematic error decreased but quantitative agreement with experiment was only reached for a few compounds. From a retrospective analysis a weak point of the correction term was identified.
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Affiliation(s)
- Daniel Markthaler
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, 70569, Stuttgart, Germany
| | - Hamzeh Kraus
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, 70569, Stuttgart, Germany
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, 70569, Stuttgart, Germany.
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13
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Brockett AT, Deng C, Shuster M, Perera S, DiMaggio D, Cheng M, Murkli S, Briken V, Roesch MR, Isaacs L. In Vitro and In Vivo Sequestration of Methamphetamine by a Sulfated Acyclic CB[n]-Type Receptor. Chemistry 2021; 27:17476-17486. [PMID: 34613641 PMCID: PMC8665056 DOI: 10.1002/chem.202102919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Indexed: 01/26/2023]
Abstract
We report the synthesis of two new acyclic sulfated acyclic CB[n]-type receptors (TriM0 and Me4 TetM0) and investigations of their binding properties toward a panel of drugs of abuse (1-13) by a combination of 1 H NMR spectroscopy and isothermal titration calorimetry. TetM0 is the most potent receptor with Ka ≥106 M-1 toward methamphetamine, fentanyl, MDMA and mephedrone. TetM0 is not cytotoxic toward HepG2 and HEK 293 cells below 100 μM according to MTS metabolic and adenylate kinase release assays and is well tolerated in vivo when dosed at 46 mg kg-1 . TetM0 does not inhibit the hERG ion channel and is not mutagenic based on the Ames fluctuation test. Finally, in vivo efficacy studies show that the hyperlocomotion of mice treated with methamphetamine can be greatly reduced by treatment with TetM0 up to 5 minutes later. TetM0 has potential as a broad spectrum in vivo sequestrant for drugs of abuse.
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Affiliation(s)
- Adam T Brockett
- Department of Psychology and Program in Neuroscience and Cognitive Science (NACS), University of Maryland at College Park, College Park, MD 20742, United States
| | - Chunlin Deng
- Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, MD 20742, United States
| | - Michael Shuster
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, MD 20742, United States
| | - Suvenika Perera
- Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, MD 20742, United States
| | - Delaney DiMaggio
- Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, MD 20742, United States
| | - Ming Cheng
- Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, MD 20742, United States
| | - Steven Murkli
- Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, MD 20742, United States
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, MD 20742, United States
| | - Matthew R Roesch
- Department of Psychology and Program in Neuroscience and Cognitive Science (NACS), University of Maryland at College Park, College Park, MD 20742, United States
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, MD 20742, United States
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14
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Ghorbani M, Hudson PS, Jones MR, Aviat F, Meana-Pañeda R, Klauda JB, Brooks BR. A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge. J Comput Aided Mol Des 2021; 35:667-677. [PMID: 33939083 PMCID: PMC8131287 DOI: 10.1007/s10822-021-00385-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/12/2021] [Indexed: 12/14/2022]
Abstract
In this study, we report binding free energy calculations of various drugs-of-abuse to Cucurbit-[8]-uril as part of the SAMPL8 blind challenge. Force-field parameters were obtained from force-matching with different quantum mechanical levels of theory. The Replica Exchange Umbrella Sampling (REUS) approach was used with a cylindrical restraint to enhance the sampling of host–guest binding. Binding free energy was calculated by pulling the guest molecule from one side of the symmetric and cylindrical host, then into and through the host, and out the other side (bidirectional) as compared to pulling only to the bound pose inside the cylindrical host (unidirectional). The initial results with force-matched MP2 parameter set led to RMSE of 4.68 \documentclass[12pt]{minimal}
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\begin{document}$${\text{kcal}}/{\text{mol}}$$\end{document}kcal/mol from experimental values. However, the follow-up study with CHARMM generalized force field parameters and force-matched PM6-D3H4 parameters resulted in RMSEs from experiment of \documentclass[12pt]{minimal}
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\begin{document}$$2.65$$\end{document}2.65 and \documentclass[12pt]{minimal}
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\begin{document}$$1.72 {\text{kcal}}/{\text{mol}}$$\end{document}1.72kcal/mol, respectively, which demonstrates the potential of REUS for accurate binding free energy calculation given a more suitable description of energetics. Moreover, we compared the free energies for the so called bidirectional and unidirectional free energy approach and found that the binding free energies were highly similar. However, one issue in the bidirectional approach is the asymmetry of profile on the two sides of the host. This is mainly due to the insufficient sampling for these larger systems and can be avoided by longer sampling simulations. Overall REUS shows great promise for binding free energy calculations.
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Affiliation(s)
- Mahdi Ghorbani
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA. .,Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, 20740, USA.
| | - Phillip S Hudson
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael R Jones
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Félix Aviat
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rubén Meana-Pañeda
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, 20740, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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15
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Boz E, Stein M. Accurate Receptor-Ligand Binding Free Energies from Fast QM Conformational Chemical Space Sampling. Int J Mol Sci 2021; 22:3078. [PMID: 33802920 PMCID: PMC8002627 DOI: 10.3390/ijms22063078] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 12/22/2022] Open
Abstract
Small molecule receptor-binding is dominated by weak, non-covalent interactions such as van-der-Waals hydrogen bonding or electrostatics. Calculating these non-covalent ligand-receptor interactions is a challenge to computational means in terms of accuracy and efficacy since the ligand may bind in a number of thermally accessible conformations. The conformational rotamer ensemble sampling tool (CREST) uses an iterative scheme to efficiently sample the conformational space and calculates energies using the semi-empirical 'Geometry, Frequency, Noncovalent, eXtended Tight Binding' (GFN2-xTB) method. This combined approach is applied to blind predictions of the modes and free energies of binding for a set of 10 drug molecule ligands to the cucurbit[n]urils CB[8] receptor from the recent 'Statistical Assessment of the Modeling of Proteins and Ligands' (SAMPL) challenge including morphine, hydromorphine, cocaine, fentanyl, and ketamine. For each system, the conformational space was sufficiently sampled for the free ligand and the ligand-receptor complexes using the quantum chemical Hamiltonian. A multitude of structures makes up the final conformer-rotamer ensemble, for which then free energies of binding are calculated. For those large and complex molecules, the results are in good agreement with experimental values with a mean error of 3 kcal/mol. The GFN2-xTB energies of binding are validated by advanced density functional theory calculations and found to be in good agreement. The efficacy of the automated QM sampling workflow allows the extension towards other complex molecular interaction scenarios.
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Affiliation(s)
| | - Matthias Stein
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, 39106 Magdeburg, Germany;
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