1
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Liu H, Zhang H, IJzerman AP, Guo D. The translational value of ligand-receptor binding kinetics in drug discovery. Br J Pharmacol 2024; 181:4117-4129. [PMID: 37705429 DOI: 10.1111/bph.16241] [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: 05/19/2023] [Revised: 07/27/2023] [Accepted: 09/01/2023] [Indexed: 09/15/2023] Open
Abstract
The translation of in vitro potency of a candidate drug, as determined by traditional pharmacology metrics (such as EC50/IC50 and KD/Ki values), to in vivo efficacy and safety is challenging. Residence time, which represents the duration of drug-target interaction, can be part of a more comprehensive understanding of the dynamic nature of drug-target interactions in vivo, thereby enabling better prediction of drug efficacy and safety. As a consequence, a prolonged residence time may help in achieving sustained pharmacological activity, while transient interactions with shorter residence times may be favourable for targets associated with side effects. Therefore, integration of residence time into the early stages of drug discovery and development has yielded a number of clinical candidates with promising in vivo efficacy and safety profiles. Insights from residence time research thus contribute to the translation of in vitro potency to in vivo efficacy and safety. Further research and advances in measuring and optimizing residence time will bring a much-needed addition to the drug discovery process and the development of safer and more effective drugs. In this review, we summarize recent research progress on residence time, highlighting its importance from a translational perspective.
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Affiliation(s)
- Hongli Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Haoran Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
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2
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Kenakin T. Know your molecule: pharmacological characterization of drug candidates to enhance efficacy and reduce late-stage attrition. Nat Rev Drug Discov 2024; 23:626-644. [PMID: 38890494 DOI: 10.1038/s41573-024-00958-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 06/20/2024]
Abstract
Despite advances in chemical, computational and biological sciences, the rate of attrition of drug candidates in clinical development is still high. A key point in the small-molecule discovery process that could provide opportunities to help address this challenge is the pharmacological characterization of hit and lead compounds, culminating in the selection of a drug candidate. Deeper characterization is increasingly important, because the 'quality' of drug efficacy, at least for G protein-coupled receptors (GPCRs), is now understood to be much more than activation of commonly evaluated pathways such as cAMP signalling, with many more 'efficacies' of ligands that could be harnessed therapeutically. Such characterization is being enabled by novel assays to characterize the complex behaviour of GPCRs, such as biased signalling and allosteric modulation, as well as advances in structural biology, such as cryo-electron microscopy. This article discusses key factors in the assessments of the pharmacology of hit and lead compounds in the context of GPCRs as a target class, highlighting opportunities to identify drug candidates with the potential to address limitations of current therapies and to improve the probability of them succeeding in clinical development.
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Affiliation(s)
- Terry Kenakin
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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3
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Pinto MF, Sirina J, Holliday ND, McWhirter CL. High-throughput kinetics in drug discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100170. [PMID: 38964171 DOI: 10.1016/j.slasd.2024.100170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/21/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024]
Abstract
The importance of a drug's kinetic profile and interplay of structure-kinetic activity with PK/PD has long been appreciated in drug discovery. However, technical challenges have often limited detailed kinetic characterization of compounds to the latter stages of projects. This review highlights the advances that have been made in recent years in techniques, instrumentation, and data analysis to increase the throughput of detailed kinetic and mechanistic characterization, enabling its application earlier in the drug discovery process.
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Affiliation(s)
- Maria Filipa Pinto
- Artios Pharma Ltd, B940, Babraham Research Campus, Cambridge CB22 3FH, United Kingdom
| | - Julija Sirina
- Excellerate Bioscience Ltd, 21 The Triangle, NG2 Business Park, Nottingham, NG2 1AE, United Kingdom
| | - Nicholas D Holliday
- Excellerate Bioscience Ltd, 21 The Triangle, NG2 Business Park, Nottingham, NG2 1AE, United Kingdom; School of Life Sciences, The Medical School, University of Nottingham, Nottingham, NG7 2UH, United Kingdom
| | - Claire L McWhirter
- Artios Pharma Ltd, B940, Babraham Research Campus, Cambridge CB22 3FH, United Kingdom.
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4
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Vlachodimou A, Bouma J, De Cleyn M, Berthelot D, Pype S, Bosmans JP, van Vlijmen H, Wroblowski B, Heitman LH, IJzerman AP. Kinetic profiling of novel spirobenzo-oxazinepiperidinone derivatives as equilibrative nucleoside transporter 1 inhibitors. Purinergic Signal 2024; 20:193-205. [PMID: 37423967 PMCID: PMC10997566 DOI: 10.1007/s11302-023-09948-9] [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: 01/31/2023] [Accepted: 05/26/2023] [Indexed: 07/11/2023] Open
Abstract
Evaluation of kinetic parameters of drug-target binding, kon, koff, and residence time (RT), in addition to the traditional in vitro parameter of affinity is receiving increasing attention in the early stages of drug discovery. Target binding kinetics emerges as a meaningful concept for the evaluation of a ligand's duration of action and more generally drug efficacy and safety. We report the biological evaluation of a novel series of spirobenzo-oxazinepiperidinone derivatives as inhibitors of the human equilibrative nucleoside transporter 1 (hENT1, SLC29A1). The compounds were evaluated in radioligand binding experiments, i.e., displacement, competition association, and washout assays, to evaluate their affinity and binding kinetic parameters. We also linked these pharmacological parameters to the compounds' chemical characteristics, and learned that separate moieties of the molecules governed target affinity and binding kinetics. Among the 29 compounds tested, 28 stood out with high affinity and a long residence time of 87 min. These findings reveal the importance of supplementing affinity data with binding kinetics at transport proteins such as hENT1.
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Affiliation(s)
- Anna Vlachodimou
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Jara Bouma
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Michel De Cleyn
- Janssen Research and Development, Antwerpseweg 30, 2340, Beerse, Belgium
| | - Didier Berthelot
- Janssen Research and Development, Antwerpseweg 30, 2340, Beerse, Belgium
| | - Stefan Pype
- Janssen Research and Development, Antwerpseweg 30, 2340, Beerse, Belgium
| | - Jean-Paul Bosmans
- Janssen Research and Development, Antwerpseweg 30, 2340, Beerse, Belgium
| | - Herman van Vlijmen
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
- Janssen Research and Development, Antwerpseweg 30, 2340, Beerse, Belgium
| | | | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.
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5
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Matsunaga R, Ujiie K, Inagaki M, Fernández Pérez J, Yasuda Y, Mimasu S, Soga S, Tsumoto K. High-throughput analysis system of interaction kinetics for data-driven antibody design. Sci Rep 2023; 13:19417. [PMID: 37990030 PMCID: PMC10663500 DOI: 10.1038/s41598-023-46756-y] [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: 09/01/2023] [Accepted: 11/04/2023] [Indexed: 11/23/2023] Open
Abstract
Surface plasmon resonance (SPR) is widely used for antigen-antibody interaction kinetics analysis. However, it has not been used in the screening phase because of the low throughput of measurement and analysis. Herein, we proposed a high-throughput SPR analysis system named "BreviA" using the Brevibacillus expression system. Brevibacillus was transformed using a plasmid library containing various antibody sequences, and single colonies were cultured in 96-well plates. Sequence analysis was performed using bacterial cells, and recombinant antibodies secreted in the supernatant were immobilized on a sensor chip to analyze their interactions with antigens using high-throughput SPR. Using this system, the process from the transformation to 384 interaction analyses can be performed within a week. This system utility was tested using an interspecies specificity design of an anti-human programmed cell death protein 1 (PD-1) antibody. A plasmid library containing alanine and tyrosine mutants of all complementarity-determining region residues was generated. A high-throughput SPR analysis was performed against human and mouse PD-1, showing that the mutation in the specific region enhanced the affinity for mouse PD-1. Furthermore, deep mutational scanning of the region revealed two mutants with > 100-fold increased affinity for mouse PD-1, demonstrating the potential efficacy of antibody design using data-driven approach.
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Affiliation(s)
- Ryo Matsunaga
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
| | - Kan Ujiie
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
| | - Mayuko Inagaki
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
| | - Jorge Fernández Pérez
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
| | - Yoshiki Yasuda
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
| | - Shinya Mimasu
- Biologics Engineering, Discovery Intelligence, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi, Ibaraki, 305-8585, Japan
| | - Shinji Soga
- Biologics Engineering, Discovery Intelligence, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi, Ibaraki, 305-8585, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
- The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
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6
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Sharma S, Joshi S, Kalidindi T, Digwal CS, Panchal P, Lee SG, Zanzonico P, Pillarsetty N, Chiosis G. Unraveling the Mechanism of Epichaperome Modulation by Zelavespib: Biochemical Insights on Target Occupancy and Extended Residence Time at the Site of Action. Biomedicines 2023; 11:2599. [PMID: 37892973 PMCID: PMC10604720 DOI: 10.3390/biomedicines11102599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Drugs with a long residence time at their target sites are often more efficacious in disease treatment. The mechanism, however, behind prolonged retention at the site of action is often difficult to understand for non-covalent agents. In this context, we focus on epichaperome agents, such as zelavespib and icapamespib, which maintain target binding for days despite rapid plasma clearance, minimal retention in non-diseased tissues, and rapid metabolism. They have shown significant therapeutic value in cancer and neurodegenerative diseases by disassembling epichaperomes, which are assemblies of tightly bound chaperones and other factors that serve as scaffolding platforms to pathologically rewire protein-protein interactions. To investigate their impact on epichaperomes in vivo, we conducted pharmacokinetic and target occupancy measurements for zelavespib and monitored epichaperome assemblies biochemically in a mouse model. Our findings provide evidence of the intricate mechanism through which zelavespib modulates epichaperomes in vivo. Initially, zelavespib becomes trapped when epichaperomes bound, a mechanism that results in epichaperome disassembly, with no change in the expression level of epichaperome constituents. We propose that the initial trapping stage of epichaperomes is a main contributing factor to the extended on-target residence time observed for this agent in clinical settings. Zelavespib's residence time in tumors seems to be dictated by target disassembly kinetics rather than by frank drug-target unbinding kinetics. The off-rate of zelavespib from epichaperomes is, therefore, much slower than anticipated from the recorded tumor pharmacokinetic profile or as determined in vitro using diluted systems. This research sheds light on the underlying processes that make epichaperome agents effective in the treatment of certain diseases.
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Affiliation(s)
- Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
| | - Suhasini Joshi
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
| | - Teja Kalidindi
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (T.K.); (S.-G.L.); (P.Z.)
| | - Chander S. Digwal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
| | - Palak Panchal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
| | - Sang-Gyu Lee
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (T.K.); (S.-G.L.); (P.Z.)
| | - Pat Zanzonico
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (T.K.); (S.-G.L.); (P.Z.)
| | - Nagavarakishore Pillarsetty
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; (T.K.); (S.-G.L.); (P.Z.)
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA (S.J.); (C.S.D.); (P.P.)
- Breast Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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7
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Abbasi M, Sohail M, Minhas MU, Mahmood A, Shah SA, Munir A, Kashif MUR. Folic acid-decorated alginate nanoparticles loaded hydrogel for the oral delivery of diferourylmethane in colorectal cancer. Int J Biol Macromol 2023; 233:123585. [PMID: 36758757 DOI: 10.1016/j.ijbiomac.2023.123585] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/25/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
Abstract
The disease-related suffering in colorectal cancer remains prevalent despite advancements in the field of drug delivery. Chemotherapy-related side effects and non-specificity remain a challenge in drug delivery. The great majority of hydrophobic drugs cannot be successfully delivered to the colon orally mainly due to poor solubility, low bioavailability, pH differences, and food interactions. Polymeric nanoparticles are potential drug delivery candidates but there are numerous limitations to their usefulness in colon cancer. The nanoparticles are removed from the body rapidly by p-glycoprotein efflux, inactivation, or breakdown by enzymes limiting their efficiency. Furthermore, there is a lack of selectivity in targeting cancer cells; nanoparticles may also target healthy cells, resulting in toxicity and adverse effects. The study aimed to use nanoparticles for specific targeting of the colorectal tumor cells via the oral route of administration without adverse effects. Folic acid (FA), a cancer-targeting ligand possessing a high affinity for folate receptors overexpressed in colorectal cancers was conjugated to sodium alginate- nanoparticles by NH2-linkage. The folic-acid conjugated nanoparticles (FNPs) were delivered to the colon by a pH-sensitive hydrogel synthesized by the free radical polymerization method to provide sustained drug release. The developed system referred to as the "Hydrogel-Nano (HN) drug delivery system," was specifically capable of delivering diferourylmethane to the colon. The HN system was characterized by DLS, FTIR, XRD, TGA, DSC, and SEM. The FNPs size, polydispersity index, and zeta potential were measured. The folic acid-conjugation to nanoparticles' surface was studied by UV-visible spectroscopy using Beer-Lambert's law. In-vitro studies, including sol-gel, porosity, drug loading, entrapment efficiency, etc., revealed promising results. The swelling and release studies showed pH-dependent release of the drug in colonic pH 7.4. Cellular uptake and cytotoxicity studies performed on FR-overexpressed Hela cell lines and FR-negative A-549 cell lines showed facilitated uptake of nanoparticles by folate receptors. A threefold increase in Cmax and prolongation of the mean residence time (MRT) to 14.52 +/- 0.217 h indicated sustained drug release by the HN system. The findings of the study can provide a sufficient ground that the synergistic approach of the HN system can deliver hydrophobic drugs to colorectal cancer cells via the oral route, but further in-vivo animal cancer model studies are required.
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Affiliation(s)
- Mudassir Abbasi
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, Abbottabad 22060, KPK, Pakistan
| | - Muhammad Sohail
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, Abbottabad 22060, KPK, Pakistan; Faculty of Pharmacy, Cyprus International University, Nicosia, 99258, North Cyprus.
| | | | - Arshad Mahmood
- Collage of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates; AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Syed Ahmed Shah
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, Abbottabad 22060, KPK, Pakistan; Department of Pharmaceutical Sciences, The Superior University, Lahore 54600, Pakistan
| | - Abubakar Munir
- Department of Pharmaceutical Sciences, The Superior University, Lahore 54600, Pakistan
| | - Mehboob-Ur-Rehman Kashif
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, Abbottabad 22060, KPK, Pakistan
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Li X, Yang W, Chen H, Pan F, Liu W, Qi D, Yu S, Liu H, Chai X, Liu Y, Pan Y, Wang G. Rapid screening and in vivo target occupancy quantitative evaluation of xanthine oxidase inhibitors based on drug-target binding kinetics research strategy: A case study of Chrysanthemum morifolium Ramat. Biomed Pharmacother 2023; 161:114379. [PMID: 36827711 DOI: 10.1016/j.biopha.2023.114379] [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: 11/30/2022] [Revised: 01/26/2023] [Accepted: 02/05/2023] [Indexed: 02/24/2023] Open
Abstract
Chrysanthemum morifolium Ramat. is a kind of food and drug dual-use traditional Chinese medicine possessing multiple pharmacological and biochemical benefits. In our study, a rapid and high-throughput method based on Surface plasmon resonance (SPR) biosensor technology was developed and verified for screening potential xanthine oxidase (XOD) inhibitors exemplarily in the Chrysanthemum morifolium Ramat. Coupled with ultra-high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS), 14 XOD-binders were identified. In the SPR-based biosensor and molecular docking analysis, most compounds exhibited a strong affinity and binding kinetic property (association rate constant, Kon and dissociation rate constant, Koff) for XOD and could be regarded as potential inhibitors. More importantly, to further accurately assess target occupancy of candidate compounds in vivo, a mathematical model was established and verified involving three crucial intrinsic kinetic processes (Pharmacokinetics, Binding kinetic and Target kinetic). Overall, the proposed screening and assessment strategy could be proved an effective theoretical basis for further pharmacodynamic evaluation.
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Affiliation(s)
- Xueyan Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Wenning Yang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Hongjiao Chen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Fulu Pan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Wei Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Dongying Qi
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Shuang Yu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Huining Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Xiaoyu Chai
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yang Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China.
| | - Yanli Pan
- Institute of Information on Traditional Chinese Medicine China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Guopeng Wang
- Zhongcai Health (Beijing) Biological Technology Development Co., Ltd., Beijing 101500, China.
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9
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Ziada S, Diharce J, Raimbaud E, Aci-Sèche S, Ducrot P, Bonnet P. Estimation of Drug-Target Residence Time by Targeted Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:5536-5549. [PMID: 36350238 DOI: 10.1021/acs.jcim.2c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Drug-target residence time has emerged as a key selection factor in drug discovery since the binding duration of a drug molecule to its protein target can significantly impact its in vivo efficacy. The challenge in studying the residence time, in early drug discovery stages, lies in how to cost-effectively determine the residence time for the systematic assessment of compounds. Currently, there is still a lack of computational protocols to quickly estimate such a measure, particularly for large and flexible protein targets and drugs. Here, we report an efficient computational protocol, based on targeted molecular dynamics, to rank drug candidates by their residence time and to obtain insights into ligand-target dissociation mechanisms. The method was assessed on a dataset of 10 arylpyrazole inhibitors of CDK8, a large, flexible, and clinically important target, for which the experimental residence time of the inhibitors ranges from minutes to hours. The compounds were correctly ranked according to their estimated residence time scores compared to their experimental values. The analysis of protein-ligand interactions along the dissociation trajectories highlighted the favorable contribution of hydrophobic contacts to residence time and revealed key residues that strongly affect compound residence time.
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Affiliation(s)
- Sonia Ziada
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 245067, France
| | - Julien Diharce
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 245067, France
| | - Eric Raimbaud
- Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine78290, France
| | - Samia Aci-Sèche
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 245067, France
| | - Pierre Ducrot
- Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine78290, France
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 245067, France
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10
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Chitosan/guar gum-based thermoreversible hydrogels loaded with pullulan nanoparticles for enhanced nose-to-brain drug delivery. Int J Biol Macromol 2022; 215:579-595. [PMID: 35779651 DOI: 10.1016/j.ijbiomac.2022.06.161] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Accepted: 06/25/2022] [Indexed: 11/21/2022]
Abstract
The biopolymers-based two-fold system could provide a sustained release platform for drug delivery to the brain resisting the mucociliary clearance, enzymatic degradation, bypassing the first-pass hepatic metabolism, and BBB thus providing superior bioavailability through intranasal administration. In this study, poloxamers PF-127/PF-68 grafted chitosan HCl-co-guar gum-based thermoresponsive hydrogel loaded with eletriptan hydrobromide laden pullulan nanoparticles was synthesized and subjected to dynamic light scattering, Fourier transform infrared spectroscopy, thermal analysis, x-ray diffraction, scanning electron microscopy, stability studies, mucoadhesive strength and time, gel strength, cloud point assessment, rheological assessment, ex-vivo permeation, cell viability assay, histology studies, and in-vivo Pharmacokinetics studies, etc. It is quite evident that CSG-EH-NPs T-Hgel has an enhanced sustained release drug profile where approximately 86 % and 84 % of drug released in phosphate buffer saline and simulated nasal fluid respectively throughout 48 h compared to EH-NPs where 99.44 % and 97.53 % of the drug was released in PBS and SNF for 8 h. In-vivo PKa parameters i.e., mean residence time (MRT) of 11.9 ± 0.83 compared to EH-NPs MRT of 10.2 ± 0.92 and area under the curve (AUCtot) of 42,540.5 ± 5314.14 comparing to AUCtot of EH-NPs 38,026 ± 6343.1 also establish the superiority of CSG-EH-NPs T-Hgel.
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11
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Wu X, Xu LY, Li EM, Dong G. Application of molecular dynamics simulation in biomedicine. Chem Biol Drug Des 2022; 99:789-800. [PMID: 35293126 DOI: 10.1111/cbdd.14038] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/25/2022] [Accepted: 03/05/2022] [Indexed: 02/05/2023]
Abstract
Molecular dynamics (MD) simulation has been widely used in the field of biomedicine to study the conformational transition of proteins caused by mutation or ligand binding/unbinding. It provides some perspectives those are difficult to find in traditional biochemical or pathological experiments, for example, detailed effects of mutations on protein structure and protein-protein/ligand interaction at the atomic level. In this review, a broad overview on conformation changes and drug discovery by MD simulation is given. We first discuss the preparation of protein structure for MD simulation, which is a key step that determines the accuracy of the simulation. Then, we summarize the applications of commonly used force fields and MD simulations in scientific research. Finally, enhanced sampling methods and common applications of these methods are introduced. In brief, MD simulation is a powerful tool and it can be used to guide experimental study. The combination of MD simulation and experimental techniques is an a priori means to solve the biomedical problems and give a deep understanding on the relationship between protein structure and function.
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Affiliation(s)
- Xiaodong Wu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Li-Yan Xu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
| | - Geng Dong
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
- Medical Informatics Research Center, Shantou University Medical College, Shantou, China
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12
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Abbasi M, Sohail M, Minhas MU, Iqbal J, Mahmood A, Shaikh AJ. Folic acid-functionalized nanoparticles-laden biomaterials for the improved oral delivery of hydrophobic drug in colorectal cancer. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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13
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Vlachodimou A, de Vries H, Pasoli M, Goudswaard M, Kim SA, Kim YC, Scortichini M, Marshall M, Linden J, Heitman LH, Jacobson KA, IJzerman AP. Kinetic profiling and functional characterization of 8-phenylxanthine derivatives as A 2B adenosine receptor antagonists. Biochem Pharmacol 2022; 200:115027. [PMID: 35395239 DOI: 10.1016/j.bcp.2022.115027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022]
Abstract
A2B adenosine receptor (A2BAR) antagonists have therapeutic potential in inflammation-related diseases such as asthma, chronic obstructive pulmonary disease and cancer. However, no drug is currently clinically approved, creating a demand for research on novel antagonists. Over the last decade, the study of target binding kinetics, along with affinity and potency, has been proven valuable in early drug discovery stages, as it is associated with improved in vivo drug efficacy and safety. In this study, we report the synthesis and biological evaluation of a series of xanthine derivatives as A2BAR antagonists, including an isothiocyanate derivative designed to bind covalently to the receptor. All 28 final compounds were assessed in radioligand binding experiments, to evaluate their affinity and for those qualifying, kinetic binding parameters. Both structure-affinity and structure-kinetic relationships were derived, providing a clear relationship between affinity and dissociation rate constants. Two structurally similar compounds, 17 and 18, were further evaluated in a label-free assay due to their divergent kinetic profiles. An extended cellular response was associated with long A2BAR residence times. This link between a ligand's A2BAR residence time and its functional effect highlights the importance of binding kinetics as a selection parameter in the early stages of drug discovery.
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Affiliation(s)
- Anna Vlachodimou
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, the Netherlands
| | - Henk de Vries
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, the Netherlands
| | - Milena Pasoli
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, the Netherlands
| | - Miranda Goudswaard
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, the Netherlands
| | - Soon-Ai Kim
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Yong-Chul Kim
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Mirko Scortichini
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Melissa Marshall
- Department of Internal Medicine and Molecular Physiology & Biological Physics, University of Virginia Health Science Center, Charlottesville, VA 22908, USA
| | - Joel Linden
- Department of Internal Medicine and Molecular Physiology & Biological Physics, University of Virginia Health Science Center, Charlottesville, VA 22908, USA
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, the Netherlands; Oncode Institute, Leiden, the Netherlands
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, 9000 Rockville Pike, Bethesda, MD 20892, USA.
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, the Netherlands.
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14
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IJzerman AP, Jacobson KA, Müller CE, Cronstein BN, Cunha RA. International Union of Basic and Clinical Pharmacology. CXII: Adenosine Receptors: A Further Update. Pharmacol Rev 2022; 74:340-372. [PMID: 35302044 PMCID: PMC8973513 DOI: 10.1124/pharmrev.121.000445] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Our previous International Union of Basic and Clinical Pharmacology report on the nomenclature and classification of adenosine receptors (2011) contained a number of emerging developments with respect to this G protein-coupled receptor subfamily, including protein structure, protein oligomerization, protein diversity, and allosteric modulation by small molecules. Since then, a wealth of new data and results has been added, allowing us to explore novel concepts such as target binding kinetics and biased signaling of adenosine receptors, to examine a multitude of receptor structures and novel ligands, to gauge new pharmacology, and to evaluate clinical trials with adenosine receptor ligands. This review should therefore be considered a further update of our previous reports from 2001 and 2011. SIGNIFICANCE STATEMENT: Adenosine receptors (ARs) are of continuing interest for future treatment of chronic and acute disease conditions, including inflammatory diseases, neurodegenerative afflictions, and cancer. The design of AR agonists ("biased" or not) and antagonists is largely structure based now, thanks to the tremendous progress in AR structural biology. The A2A- and A2BAR appear to modulate the immune response in tumor biology. Many clinical trials for this indication are ongoing, whereas an A2AAR antagonist (istradefylline) has been approved as an anti-Parkinson agent.
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Affiliation(s)
- Adriaan P IJzerman
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Kenneth A Jacobson
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Christa E Müller
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Bruce N Cronstein
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Rodrigo A Cunha
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
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15
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Srinivasan B. A guide to enzyme kinetics in early drug discovery. FEBS J 2022; 290:2292-2305. [PMID: 35175693 DOI: 10.1111/febs.16404] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 12/28/2022]
Abstract
Drugs interact with their target of interest to bring about the desired phenotypic outcome that results in disease alleviation. Traditionally, most lead optimization exercises were driven by affinity measures (like IC50 ) to inform structure-activity relationship (SAR)-guided medicinal chemistry. However, an IC50 value is a thermodynamic estimate measured under equilibrium conditions that can vary as a function of substrate concentration and/or time (the latter especially for nonequilibrium modalities). Further, like other thermodynamic estimates, it is a state-function that is indifferent to the path traversed from the initial state to the final state. This can be a cause for concern in drug discovery given the predominance of nonequilibrium interactions and the open thermodynamic nature of the human system. Under such situations, employing rates along with equilibrium constants (or IC50 values) would be far more relevant to capture the time evolution of the small molecule's interaction with the target of interest. These rates are generally typified by the rate of association, rate of dissociation and the residence time of the small molecule on the target (target occupancy). These parameters, when combined with the concept of target vulnerability, therapeutic window, pharmacokinetic profile of the small molecule, estimates of endogenous ligand and target turnover, will shed critical insights into the kinetics and dynamics of a small molecule's interaction with the protein, and allow realistic modelling of the system to enable optimizations and dosing decisions. With that aim, this guide will attempt to introduce the traditional role of mechanistic enzymology within drug discovery and emphasize the importance of kinetics in guiding SAR-based optimizations. It will also present initial ideas on how kinetic investigation should be positioned relative to the temporal span of a drug-discovery pipeline to leverage maximal utility from the investment in time and effort.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic and Structural Biology Discovery Sciences R&D AstraZeneca Cambridge UK
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16
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Quader S, Kataoka K, Cabral H. Nanomedicine for brain cancer. Adv Drug Deliv Rev 2022; 182:114115. [PMID: 35077821 DOI: 10.1016/j.addr.2022.114115] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 12/18/2021] [Accepted: 01/12/2022] [Indexed: 02/06/2023]
Abstract
CNS tumors remain among the deadliest forms of cancer, resisting conventional and new treatment approaches, with mortality rates staying practically unchanged over the past 30 years. One of the primary hurdles for treating these cancers is delivering drugs to the brain tumor site in therapeutic concentration, evading the blood-brain (tumor) barrier (BBB/BBTB). Supramolecular nanomedicines (NMs) are increasingly demonstrating noteworthy prospects for addressing these challenges utilizing their unique characteristics, such as improving the bioavailability of the payloadsviacontrolled pharmacokinetics and pharmacodynamics, BBB/BBTB crossing functions, superior distribution in the brain tumor site, and tumor-specific drug activation profiles. Here, we review NM-based brain tumor targeting approaches to demonstrate their applicability and translation potential from different perspectives. To this end, we provide a general overview of brain tumor and their treatments, the incidence of the BBB and BBTB, and their role on NM targeting, as well as the potential of NMs for promoting superior therapeutic effects. Additionally, we discuss critical issues of NMs and their clinical trials, aiming to bolster the potential clinical applications of NMs in treating these life-threatening diseases.
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Affiliation(s)
- Sabina Quader
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 212-0821, Japan
| | - Kazunori Kataoka
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 212-0821, Japan.
| | - Horacio Cabral
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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17
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Lay CS, Thomas DA, Evans JP, Campbell M, McCombe K, Phillipou AN, Gordon LJ, Jones EJ, Riching K, Mahmood M, Messenger C, Carver CE, Gatfield KM, Craggs PD. Development of an intracellular quantitative assay to measure compound binding kinetics. Cell Chem Biol 2022; 29:287-299.e8. [PMID: 34520747 DOI: 10.1016/j.chembiol.2021.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 06/09/2021] [Accepted: 07/23/2021] [Indexed: 02/08/2023]
Abstract
Contemporary drug discovery typically quantifies the effect of a molecule on a biological target using the equilibrium-derived measurements of IC50, EC50, or KD. Kinetic descriptors of drug binding are frequently linked with the effectiveness of a molecule in modulating a disease phenotype; however, these parameters are yet to be fully adopted in early drug discovery. Nanoluciferase bioluminescence resonance energy transfer (NanoBRET) can be used to measure interactions between fluorophore-conjugated probes and luciferase fused target proteins. Here, we describe an intracellular NanoBRET competition assay that can be used to quantify cellular kinetic rates of compound binding to nanoluciferase-fused bromodomain and extra-terminal (BET) proteins. Comparative rates are generated using a cell-free NanoBRET assay and by utilizing orthogonal recombinant protein-based methodologies. A screen of known pan-BET inhibitors is used to demonstrate the value of this approach in the investigation of kinetic selectivity between closely related proteins.
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Affiliation(s)
- Charles S Lay
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Daniel A Thomas
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK; Arctoris, Oxford OX14 4SA, UK
| | - John P Evans
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Matthew Campbell
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Kristopher McCombe
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK; Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Alexander N Phillipou
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Laurie J Gordon
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Emma J Jones
- Protein and Cellular Sciences, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | | | - Mahnoor Mahmood
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Cassie Messenger
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Charlotte E Carver
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Kelly M Gatfield
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Peter D Craggs
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK; GSK-Francis Crick Institute Linklabs, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK.
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18
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Penna E, Niso M, Podlewska S, Volpicelli F, Crispino M, Perrone-Capano C, Bojarski AJ, Lacivita E, Leopoldo M. In Vitro and In Silico Analysis of the Residence Time of Serotonin 5-HT 7 Receptor Ligands with Arylpiperazine Structure: A Structure-Kinetics Relationship Study. ACS Chem Neurosci 2022; 13:497-509. [PMID: 35099177 DOI: 10.1021/acschemneuro.1c00710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
During the last decade, the kinetics of drug-target interaction has received increasing attention as an important pharmacological parameter in the drug development process. Several studies have suggested that the lipophilicity of a molecule can play an important role. To date, this aspect has been studied for several G protein-coupled receptors (GPCRs) ligands but not for the 5-HT7 receptor (5-HT7R), a GPCR proposed as a valid therapeutic target in neurodevelopmental and neuropsychiatric disorders associated with abnormal neuronal connectivity. In this study, we report on structure-kinetics relationships of a set of arylpiperazine-based 5-HT7R ligands. We found that it is not the overall lipophilicity of the molecule that influences drug-target interaction kinetics but rather the position of polar groups within the molecule. Next, we performed a combination of molecular docking studies and molecular dynamics simulations to gain insights into structure-kinetics relationships. These studies did not suggest specific contact patterns between the ligands and the receptor-binding site as determinants for compounds kinetics. Finally, we compared the abilities of two 5-HT7R agonists with similar receptor-binding affinities and different residence times to stimulate the 5-HT7R-mediated neurite outgrowth in mouse neuronal primary cultures and found that the compounds induced the effect with different timing. This study provides the first insights into the binding kinetics of arylpiperazine-based 5-HT7R ligands that can be helpful to design new 5-HT7R ligands with fine-tuning of the kinetic profile.
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Affiliation(s)
- Eduardo Penna
- Department of Biology, University of Naples Federico II, via Cintia 26, 80126 Naples, Italy
- Biofordrug srl, via Dante 99, 70019 Triggiano (Bari), Italy
| | - Mauro Niso
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona 4, 70125 Bari, Italy
| | - Sabina Podlewska
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343 Kraków, Poland
| | - Floriana Volpicelli
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
| | - Marianna Crispino
- Department of Biology, University of Naples Federico II, via Cintia 26, 80126 Naples, Italy
| | - Carla Perrone-Capano
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, National Research Council (CNR), via Pietro Castellino 111, 80131 Naples, Italy
| | - Andrzej J. Bojarski
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, 31-343 Kraków, Poland
| | - Enza Lacivita
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona 4, 70125 Bari, Italy
| | - Marcello Leopoldo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona 4, 70125 Bari, Italy
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19
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Distinct In Vitro Binding Profile of the Somatostatin Receptor Subtype 2 Antagonist [ 177Lu]Lu-OPS201 Compared to the Agonist [ 177Lu]Lu-DOTA-TATE. Pharmaceuticals (Basel) 2021; 14:ph14121265. [PMID: 34959665 PMCID: PMC8706879 DOI: 10.3390/ph14121265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 01/14/2023] Open
Abstract
Treatment of neuroendocrine tumours with the radiolabelled somatostatin receptor subtype 2 (SST2) peptide agonist [177Lu]Lu-DOTA-TATE is effective and well-established. Recent studies suggest improved therapeutic efficacy using the SST2 peptide antagonist [177Lu]Lu-OPS201. However, little is known about the cellular mechanisms that lead to the observed differences. In the present in vitro study, we compared kinetic binding, saturation binding, competition binding, cellular uptake and release of [177Lu]Lu-OPS201 versus [177Lu]Lu-DOTA-TATE using HEK cells stably transfected with the human SST2. While [177Lu]Lu-OPS201 and [177Lu]Lu-DOTA-TATE exhibited comparable affinity (KD, 0.15 ± 0.003 and 0.08 ± 0.02 nM, respectively), [177Lu]Lu-OPS201 recognized four times more binding sites than [177Lu]Lu-DOTA-TATE. Competition assays demonstrated that a high concentration of the agonist displaced only 30% of [177Lu]Lu-OPS201 bound to HEK-SST2 cell membranes; an indication that the antagonist binds to additional sites that are not recognized by the agonist. [177Lu]Lu-OPS201 showed faster association and slower dissociation than [177Lu]Lu-DOTA-TATE. Whereas most of [177Lu]Lu-OPS201 remained at the cell surface, [177Lu]Lu-DOTA-TATE was almost completely internalised inside the cell. The present data identified distinct differences between [177Lu]Lu-OPS201 and [177Lu]Lu-DOTA-TATE regarding the recognition of receptor binding sites (higher for [177Lu]Lu-OPS201) and their kinetics (faster association and slower dissociation of [177Lu]Lu-OPS201) that explain, to a great extent, the improved therapeutic efficacy of [177Lu]Lu-OPS201 compared to [177Lu]Lu-DOTA-TATE.
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20
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Zhang Q, Zhao N, Meng X, Yu F, Yao X, Liu H. The prediction of protein-ligand unbinding for modern drug discovery. Expert Opin Drug Discov 2021; 17:191-205. [PMID: 34731059 DOI: 10.1080/17460441.2022.2002298] [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] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Drug-target thermodynamic and kinetic information have perennially important roles in drug design. The prediction of protein-ligand unbinding, which can provide important kinetic information, in experiments continues to face great challenges. Uncovering protein-ligand unbinding through molecular dynamics simulations has become efficient and inexpensive with the progress and enhancement of computing power and sampling methods. AREAS COVERED In this review, various sampling methods for protein-ligand unbinding and their basic principles are firstly briefly introduced. Then, their applications in predicting aspects of protein-ligand unbinding, including unbinding pathways, dissociation rate constants, residence time and binding affinity, are discussed. EXPERT OPINION Although various sampling methods have been successfully applied in numerous systems, they still have shortcomings and deficiencies. Most enhanced sampling methods require researchers to possess a wealth of prior knowledge of collective variables or reaction coordinates. In addition, most systems studied at present are relatively simple, and the study of complex systems in real drug research remains greatly challenging. Through the combination of machine learning and enhanced sampling methods, prediction accuracy can be further improved, and some problems encountered in complex systems also may be solved.
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Affiliation(s)
| | - Nannan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaoxiao Meng
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Fansen Yu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China.,Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
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21
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Li G, Yi B, Liu J, Jiang X, Pan F, Yang W, Liu H, Liu Y, Wang G. Effect of CYP3A4 Inhibitors and Inducers on Pharmacokinetics and Pharmacodynamics of Saxagliptin and Active Metabolite M2 in Humans Using Physiological-Based Pharmacokinetic Combined DPP-4 Occupancy. Front Pharmacol 2021; 12:746594. [PMID: 34737703 PMCID: PMC8560969 DOI: 10.3389/fphar.2021.746594] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/13/2021] [Indexed: 11/26/2022] Open
Abstract
We aimed to develop a physiological-based pharmacokinetic and dipepidyl peptidase 4 (DPP-4) occupancy model (PBPK-DO) characterized by two simultaneous simulations to predict pharmacokinetic (PK) and pharmacodynamic changes of saxagliptin and metabolite M2 in humans when coadministered with CYP3A4 inhibitors or inducers. Ketoconazole, delavirdine, and rifampicin were selected as a CYP3A4 competitive inhibitor, a time-dependent inhibitor, and an inducer, respectively. Here, we have successfully simulated PK profiles and DPP-4 occupancy profiles of saxagliptin in humans using the PBPK-DO model. Additionally, under the circumstance of actually measured values, predicted results were good and in line with observations, and all fold errors were below 2. The prediction results demonstrated that the oral dose of saxagliptin should be reduced to 2.5 mg when coadministrated with ketoconazole. The predictions also showed that although PK profiles of saxagliptin showed significant changes with delavirdine (AUC 1.5-fold increase) or rifampicin (AUC: a decrease to 0.19-fold) compared to those without inhibitors or inducers, occupancies of DPP-4 by saxagliptin were nearly unchanged, that is, the administration dose of saxagliptin need not adjust when there is coadministration with delavirdine or rifampicin.
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Affiliation(s)
- Gang Li
- Beijing Adamadle Biotech Co, Ltd., Beijing, China
| | - Bowen Yi
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jingtong Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaoquan Jiang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Fulu Pan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Wenning Yang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Haibo Liu
- Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, China
| | - Yang Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Guopeng Wang
- Zhongcai Health (Beijing) Biological Technology Development Co, Ltd., Beijing, China
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22
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Modeling the Effect of Binding Kinetics in Spatial Drug Distribution in the Brain. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:5533886. [PMID: 34285707 PMCID: PMC8275424 DOI: 10.1155/2021/5533886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/28/2021] [Accepted: 06/09/2021] [Indexed: 11/28/2022]
Abstract
A 3-dimensional mathematical model is developed to determine the effect of drug binding kinetics on the spatial distribution of a drug within the brain. The key components, namely, transport across the blood-brain barrier (BBB), drug distribution in the brain extracellular fluid (ECF), and drug binding kinetics are coupled with the bidirectional bulk flow of the brain ECF to enhance the visualization of drug concentration in the brain. The model is developed based on the cubical volume of a brain unit, which is a union of three subdomains: the brain ECF, the BBB, and the blood plasma. The model is a set of partial differential equations and the associated initial and boundary conditions through which the drug distribution process in the mentioned subdomains is described. Effects of drug binding kinetics are investigated by varying the binding parameter values for both nonspecific and specific binding sites. All variations of binding parameter values are discussed, and the results show the improved visualization of the effect of binding kinetics in the drug distribution within the brain. For more realistic visualization, we suggest incorporating more brain components that make up the large volume of the brain tissue.
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23
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Abstract
IntroductionThe pharmacological action of a drug is linked to its affinity for a specific molecular target as quantified by in vitro equilibrium measurements. However, it is clear that for many highly effective drugs, interactions with their molecular targets do not conform to simple, equilibrium conditions in vivo and this results in a temporal discordance between pharmacokinetics and pharmacodynamics. The drug-target residence time model was developed to provide a theoretical framework with which to understand cases in which very slow dissociation of the drug-target complex in vivo results in durable PD effects even after systemic concentrations of drug have waned.Area coveredIn this article, the author provides a brief description of the drug-target residence time model and focuses on the refinements that have been made to the original model to incorporate the influences of compound rebinding in cells and pharmacokinetic properties of drug molecules.Expert opinionThere is now overwhelming evidence for the utility of the drug-target residence time model as a framework for understanding in vivo drug action. The in vitro measured residence time (τR) must be used in concert with equilibrium measures of drug-target affinity (e.g. IC50) and with in vivo measures of pharmacokinetic half-life, to afford the researcher a powerful approach to compound optimization for clinical effect. Despite the significant use and refinement of this model, continued studies are required to better understand the dynamic interplay between residence time, target pathobiology, drug distribution and drug pharmacokinetics.
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24
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Shah SA, Sohail M, Minhas MU, Khan S, Hussain Z, Mahmood A, Kousar M, Thu HE, Abbasi M, Kashif MUR. Curcumin-laden hyaluronic acid-co-Pullulan-based biomaterials as a potential platform to synergistically enhance the diabetic wound repair. Int J Biol Macromol 2021; 185:350-368. [PMID: 34171251 DOI: 10.1016/j.ijbiomac.2021.06.119] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 01/13/2023]
Abstract
Injectable hydrogel with multifunctional tunable properties comprising biocompatibility, anti-oxidative, anti-bacterial, and/or anti-infection are highly preferred to efficiently promote diabetic wound repair and its development remains a challenge. In this study, we report hyaluronic acid and Pullulan-based injectable hydrogel loaded with curcumin that could potentiate reepithelization, increase angiogenesis, and collagen deposition at wound microenvironment to endorse healing cascade compared to other treatment groups. The physical interaction and self-assembly of hyaluronic acid-Pullulan-grafted-pluronic F127 injectable hydrogel were confirmed using nuclear magnetic resonance (1H NMR) and Fourier transformed infrared spectroscopy (FT-IR), and cytocompatibility was confirmed by fibroblast viability assay. The CUR-laden hyaluronic acid-Pullulan-g-F127 injectable hydrogel promptly undergoes a sol-gel transition and has proved to potentiate wound healing in a streptozotocin-induced diabetic rat model by promoting 93% of wound closure compared to other groups having 35%, 38%, and 62%. The comparative in vivo study and histological examination was conducted which demonstrated an expeditious recovery rate by significantly reducing the wound healing days i.e. 35 days in a control group, 33 days in the CUR suspension group, 21 days in unloaded injectable, and 13 days was observed in CUR loaded hydrogel group. Furthermore, we suggest that the injectable hydrogel laden with CUR showed a prompt wound healing potential by increasing the cell proliferation and serves as a drug delivery platform for sustained and targeted delivery of hydrophobic moieties.
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Affiliation(s)
- Syed Ahmed Shah
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan
| | - Muhammad Sohail
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan.
| | | | - Shahzeb Khan
- Department of Pharmacy, University of Malakand, Lower Dir, KPK, Pakistan; Discipline of Pharmaceutical Sciences, School of Health Sciences, UKZN, Durban, South Africa
| | - Zahid Hussain
- Department of Pharmaceutics & Pharmaceutical Technology, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Arshad Mahmood
- Collage of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Mubeen Kousar
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan
| | - Hnin Ei Thu
- Innoscience Research Sdn. Bhd., Suites B-5-7, Level 5, Skypark@ One City, Jalan Ust 25/1, Subang Jaya 47650, Selangor, Malaysia; Department of Pharmacology, Faculty of Medicine, Lincoln University College, Petaling Jaya 47301, Selangor, Malaysia
| | - Mudassir Abbasi
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan
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25
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Khurana P, McWilliams L, Wingfield J, Barratt D, Srinivasan B. A Novel High-Throughput FLIPR Tetra-Based Method for Capturing Highly Confluent Kinetic Data for Structure-Kinetic Relationship Guided Early Drug Discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:684-697. [PMID: 33783249 DOI: 10.1177/24725552211000676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Target engagement by small molecules is necessary for producing a physiological outcome. In the past, a lot of emphasis was placed on understanding the thermodynamics of such interactions to guide structure-activity relationships. It is becoming clearer, however, that understanding the kinetics of the interaction between a small-molecule inhibitor and the biological target [structure-kinetic relationship (SKR)] is critical for selection of the optimum candidate drug molecule for clinical trial. However, the acquisition of kinetic data in a high-throughput manner using traditional methods can be labor intensive, limiting the number of molecules that can be tested. As a result, in-depth kinetic studies are often carried out on only a small number of compounds, and usually at a later stage in the drug discovery process. Fundamentally, kinetic data should be used to drive key decisions much earlier in the drug discovery process, but the throughput limitations of traditional methods preclude this. A major limitation that hampers acquisition of high-throughput kinetic data is the technical challenge in collecting substantially confluent data points for accurate parameter estimation from time course analysis. Here, we describe the use of the fluorescent imaging plate reader (FLIPR), a charge-coupled device (CCD) camera technology, as a potential high-throughput tool for generating biochemical kinetic data with smaller time intervals. Subsequent to the design and optimization of the assay, we demonstrate the collection of highly confluent time-course data for various kinase protein targets with reasonable throughput to enable SKR-guided medicinal chemistry. We select kinase target 1 as a special case study with covalent inhibition, and demonstrate methods for rapid and detailed analysis of the resultant kinetic data for parameter estimation. In conclusion, this approach has the potential to enable rapid kinetic studies to be carried out on hundreds of compounds per week and drive project decisions with kinetic data at an early stage in drug discovery.
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Affiliation(s)
- Puneet Khurana
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Lisa McWilliams
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Jonathan Wingfield
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Derek Barratt
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Bharath Srinivasan
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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26
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Shah SA, Sohail M, Khan SA, Kousar M. Improved drug delivery and accelerated diabetic wound healing by chondroitin sulfate grafted alginate-based thermoreversible hydrogels. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 126:112169. [PMID: 34082970 DOI: 10.1016/j.msec.2021.112169] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/20/2021] [Accepted: 05/03/2021] [Indexed: 12/16/2022]
Abstract
Injectable hydrogels with multifunctional tunable properties comprising biocompatibility, anti-oxidative, anti-bacterial, and/or anti-infection are highly preferred to efficiently promote diabetic wound repair and its development remains a challenge. In this study, we report chondroitin sulphate (CS) and sodium alginate (SA)-based injectable hydrogel using solvent casting method loaded with curcumin that could potentiate reepithelization, increase angiogenesis, and collagen deposition at wound microenvironment to endorse healing cascade. The physical interaction and self-assembly of chondroitin sulfate grafted alginate (CS-Alg-g-PF127) hydrogel were confirmed using nuclear magnetic resonance (1H NMR) and Fourier transformed infrared spectroscopy (FT-IR), and cytocompatibility was confirmed by fibroblast viability assay. The Masson's trichrome (MT) and hematoxylin and eosin (H&E) results revealed that blank chondroitin sulfate grafted alginate (CS-Alg-g-PF127) and CUR loaded CS-Alg-g-PF127 hydrogel had promising tissue regenerative ability, and showing enhanced wound healing compared to other treatment groups. The controlled release of CUR from injectable hydrogel was evaluated by drug release studies and pharmacokinetic profile (PK) using high-performance liquid chromatography (HPLC) that exhibited the mean residence time (MRT) and area under the curve (AUC) was increased up to 16.18 h and 203.64 ± 30.1 μg/mL*h, respectively. Cytotoxicity analysis of the injectable hydrogels using 3 T3-L1 fibroblasts cells and in vivo toxicity evaluated by subcutaneous injection for 24 h followed by histological examination, confirmed good biocompatibility of CUR loaded CS-Alg-g-PF127 hydrogel. Interestingly, the results of in vivo wound healing by injectable hydrogel showed the upregulation of fibroblasts-like cells, collagen deposition, and differentiated keratinocytes stimulating dermo-epidermal junction, which might endorse that they are potential candidates for excisional wound healing models.
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Affiliation(s)
- Syed Ahmed Shah
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan
| | - Muhammad Sohail
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan.
| | - Shujaat Ali Khan
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan
| | - Mubeen Kousar
- Department of Pharmacy, COMSATS University, Islamabad, Abbottabad Campus, 22010, Pakistan
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27
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Feng B, Sundin E, Lincoln P, Mårtensson AKF. DNA threading intercalation of enantiopure [Ru(phen) 2bidppz] 2+ induced by hydrophobic catalysis. Phys Chem Chem Phys 2021; 23:2238-2244. [PMID: 33439155 DOI: 10.1039/d0cp00845a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The enantiomers of a novel mononuclear ruthenium(ii) complex [Ru(phen)2bidppz]2+ with an elongated dppz moiety were synthesized. Surprisingly, the complex showed no DNA intercalating capability in an aqueous environment. However, by the addition of water-miscible polyethylene glycol ether PEG-400, self-aggregation of the hydrophobic ruthenium(ii) complexes was counter-acted, thus strongly promoting the DNA intercalation binding mode. This mild alteration of the environment surrounding the DNA polymer does not damage or alter the DNA structure but instead enables more efficient binding characterization studies of potential DNA binding drugs.
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Affiliation(s)
- Bobo Feng
- Department of Chemistry and Chemical Engineering, Kemigården 4, SE-412 96 Gothenburg, Sweden.
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28
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Rufer AC. Drug discovery for enzymes. Drug Discov Today 2021; 26:875-886. [PMID: 33454380 DOI: 10.1016/j.drudis.2021.01.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/21/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
Enzymes are essential, physiological catalysts involved in all processes of life, including metabolism, cellular signaling and motility, as well as cell growth and division. They are attractive drug targets because of the presence of defined substrate-binding pockets, which can be exploited as binding sites for pharmaceutical enzyme inhibitors. Understanding the reaction mechanisms of enzymes and the molecular mode of action of enzyme inhibitors is indispensable for the discovery and development of potent, efficacious, and safe novel drugs. The combination of classical concepts of enzymology with new experimental and data analysis methods opens new routes for drug discovery.
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Affiliation(s)
- Arne Christian Rufer
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 065/208A, 4070 Basel, Switzerland.
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29
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Tóth AD, Garger D, Prokop S, Soltész-Katona E, Várnai P, Balla A, Turu G, Hunyady L. A general method for quantifying ligand binding to unmodified receptors using Gaussia luciferase. J Biol Chem 2021; 296:100366. [PMID: 33545176 PMCID: PMC7950324 DOI: 10.1016/j.jbc.2021.100366] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 11/23/2022] Open
Abstract
Reliable measurement of ligand binding to cell surface receptors is of outstanding biological and pharmacological importance. Resonance energy transfer-based assays are powerful approaches to achieve this goal, but the currently available methods are hindered by the necessity of receptor tagging, which can potentially alter ligand binding properties. Therefore, we developed a tag-free system to measure ligand‒receptor interactions in live cells using the Gaussia luciferase (GLuc) as a bioluminescence resonance energy transfer donor. GLuc is as small as the commonly applied Nanoluciferase but has enhanced brightness, and its proper substrate is the frequently used coelenterazine. In our assay, bystander bioluminescence resonance energy transfer is detected between a GLuc-based extracellular surface biosensor and fluorescent ligands bound to their unmodified receptors. The broad spectrum of applications includes equilibrium and kinetic ligand binding measurements for both labeled and competitive unlabeled ligands, and the assay can be utilized for different classes of plasma membrane receptors. Furthermore, the assay is suitable for high-throughput screening, as evidenced by the identification of novel α1 adrenergic receptor ligands. Our data demonstrate that GLuc-based biosensors provide a simple, sensitive, and cost-efficient platform for drug characterization and development.
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Affiliation(s)
- András Dávid Tóth
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; MTA-SE Laboratory of Molecular Physiology, Eötvös Loránd Research Network, Budapest, Hungary; Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Dániel Garger
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Susanne Prokop
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; Szentágothai János Doctoral School of Neuroscience, Semmelweis University, Budapest, Hungary
| | - Eszter Soltész-Katona
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; MTA-SE Laboratory of Molecular Physiology, Eötvös Loránd Research Network, Budapest, Hungary
| | - Péter Várnai
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; MTA-SE Laboratory of Molecular Physiology, Eötvös Loránd Research Network, Budapest, Hungary
| | - András Balla
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; MTA-SE Laboratory of Molecular Physiology, Eötvös Loránd Research Network, Budapest, Hungary
| | - Gábor Turu
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; MTA-SE Laboratory of Molecular Physiology, Eötvös Loránd Research Network, Budapest, Hungary
| | - László Hunyady
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; MTA-SE Laboratory of Molecular Physiology, Eötvös Loránd Research Network, Budapest, Hungary.
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30
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Dijon NC, Nesheva DN, Holliday ND. Luciferase Complementation Approaches to Measure GPCR Signaling Kinetics and Bias. Methods Mol Biol 2021; 2268:249-274. [PMID: 34085274 DOI: 10.1007/978-1-0716-1221-7_17] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
An understanding of the kinetic contributions to G protein-coupled receptor pharmacology and signaling is increasingly important in compound profiling. Nonequilibrium conditions are commonly present in vivo, for example, as the drug competes with dynamic changes in hormone or neurotransmitter concentration for the receptor. Under such conditions individual binding kinetic properties of the ligands can influence duration of action, local ligand concentration, and functional properties such as the degree of insurmountable inhibition. Mapping the kinetic patterns of GPCR signaling events elicited by agonists, rather than a peak response at a single timepoint, is often key to predicting their functional impact. This is also a path to a better understanding of the origins of ligand bias, and whether such ligands demonstrate their effects through selection of distinct GPCR conformations, or via their kinetic properties. Recent developments in complementation approaches, based on a small bright shrimp luciferase Nanoluc, provide a new route to kinetic analysis of GPCR signaling in living cells that is amenable to the throughput required for compound profiling. In the NanoBiT luciferase complementation system, GPCRs and effector proteins are tagged with Nanoluc fragments optimized for their low interacting affinity and stability. The interactions brought about by GPCR recruitment of the effector are reproduced by a rapid and reversible increase in NanoBiT luminescence, in the presence of its substrate furimazine. Here we discuss the methods for optimizing and validating the GPCR NanoBiT assays, and protocols for their application to study endpoint and kinetic aspects of agonist and antagonist pharmacology. We also describe how timecourse families of agonist concentration response curves, derived from a single NanoBiT assay experiment, can be used to evaluate the kinetic components in operational model derived parameters of ligand bias.
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Affiliation(s)
- Nicola C Dijon
- School of Life Sciences, The Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK.,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, Nottingham, UK
| | - Desislava N Nesheva
- School of Life Sciences, The Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK.,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, Nottingham, UK
| | - Nicholas D Holliday
- School of Life Sciences, The Medical School, Queen's Medical Centre, University of Nottingham, Nottingham, UK. .,Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, Nottingham, UK. .,Excellerate Bioscience, Biocity, Nottingham, UK.
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31
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Vendel E, Rottschäfer V, de Lange ECM. A 3D brain unit model to further improve prediction of local drug distribution within the brain. PLoS One 2020; 15:e0238397. [PMID: 32966285 PMCID: PMC7511021 DOI: 10.1371/journal.pone.0238397] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/15/2020] [Indexed: 12/14/2022] Open
Abstract
The development of drugs targeting the brain still faces a high failure rate. One of the reasons is a lack of quantitative understanding of the complex processes that govern the pharmacokinetics (PK) of a drug within the brain. While a number of models on drug distribution into and within the brain is available, none of these addresses the combination of factors that affect local drug concentrations in brain extracellular fluid (brain ECF). Here, we develop a 3D brain unit model, which builds on our previous proof-of-concept 2D brain unit model, to understand the factors that govern local unbound and bound drug PK within the brain. The 3D brain unit is a cube, in which the brain capillaries surround the brain ECF. Drug concentration-time profiles are described in both a blood-plasma-domain and a brain-ECF-domain by a set of differential equations. The model includes descriptions of blood plasma PK, transport through the blood-brain barrier (BBB), by passive transport via paracellular and transcellular routes, and by active transport, and drug binding kinetics. The impact of all these factors on ultimate local brain ECF unbound and bound drug concentrations is assessed. In this article we show that all the above mentioned factors affect brain ECF PK in an interdependent manner. This indicates that for a quantitative understanding of local drug concentrations within the brain ECF, interdependencies of all transport and binding processes should be understood. To that end, the 3D brain unit model is an excellent tool, and can be used to build a larger network of 3D brain units, in which the properties for each unit can be defined independently to reflect local differences in characteristics of the brain.
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Affiliation(s)
- Esmée Vendel
- Mathematical Institute, Leiden University, Leiden, The Netherlands
| | - Vivi Rottschäfer
- Mathematical Institute, Leiden University, Leiden, The Netherlands
- * E-mail: (VR); (EL)
| | - Elizabeth C. M. de Lange
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
- * E-mail: (VR); (EL)
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32
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Schuetz DA, Richter L, Martini R, Ecker GF. A structure-kinetic relationship study using matched molecular pair analysis. RSC Med Chem 2020; 11:1285-1294. [PMID: 34085042 PMCID: PMC8126976 DOI: 10.1039/d0md00178c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The lifetime of a binary drug–target complex is increasingly acknowledged as an important parameter for drug efficacy and safety. With a better understanding of binding kinetics and better knowledge about kinetic parameter optimization, intentionally induced prolongation of the drug–target residence time through structural changes of the ligand could become feasible. In this study we assembled datasets from 21 publications and the K4DD (Kinetic for Drug Discovery) database to conduct large scale data analysis. This resulted in 3812 small molecules annotated to 78 different targets from five protein classes (GPCRs: 273, kinases: 3238, other enzymes: 240, HSPs: 160, ion channels: 45). Performing matched molecular pair (MMP) analysis to further investigate the structure–kinetic relationship (SKR) in this data collection allowed us to identify a fundamental contribution of a ligand's polarity to its association rate, and in selected cases, also to its dissociation rate. However, we furthermore observed that the destabilization of the transition state introduced by increased polarity is often accompanied by simultaneous destabilization of the ground state resulting in an unaffected or even worsened residence time. Supported by a set of case studies, we provide concepts on how to alter ligands in ways to trigger on-rates, off-rates, or both. A large-scale study employing matched molecular pair (MMP) analysis to uncover the contribution of a compound's polarity to its association and dissociation rates.![]()
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Affiliation(s)
- Doris A Schuetz
- Department of Pharmaceutical Chemistry, University of Vienna UZA 2, Althanstrasse 14 1090 Vienna Austria
| | - Lars Richter
- Department of Pharmaceutical Chemistry, University of Vienna UZA 2, Althanstrasse 14 1090 Vienna Austria
| | - Riccardo Martini
- Department of Pharmaceutical Chemistry, University of Vienna UZA 2, Althanstrasse 14 1090 Vienna Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Chemistry, University of Vienna UZA 2, Althanstrasse 14 1090 Vienna Austria
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33
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Du Y, Wang R. Revealing the Unbinding Kinetics and Mechanism of Type I and Type II Protein Kinase Inhibitors by Local-Scaled Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:6620-6632. [PMID: 32841004 DOI: 10.1021/acs.jctc.0c00342] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein kinase inhibitors disrupt phosphorylation of the target kinases, which are an important class of drug for treating cancer and other diseases. Conventional structure-based design methods (such as molecular docking) focus on the static binding mode of the kinase inhibitor with its target. However, dissociation kinetic properties of a drug molecule are found to correlate with its residence time in vivo and thus have drawn the attention of drug designers in recent years. In this study, we have applied the local-scaled molecular dynamics (MD) simulation enabled in GROMACS software to explore the unbinding mechanism of a total of 41 type I and type II kinase inhibitors. Our simulation considered multiple starting configurations as well as possible protonation states of kinase inhibitors. Based on our local-scaled MD results, we discovered that the integrals of the favorable binding energy during dissociation correlated well (R2 = 0.64) with the experimental dissociation rate constants of those kinase inhibitors on the entire data set. Given its accuracy and technical advantage, this method may serve as a practical option for estimating this important property in reality. Our simulation also provided a reasonable explanation of the dynamic properties of kinase and its inhibitor as well as the role of relevant water molecules in dissociation.
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Affiliation(s)
- Yu Du
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China.,Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
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34
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Vendel E, Rottschäfer V, de Lange ECM. The 3D Brain Unit Network Model to Study Spatial Brain Drug Exposure under Healthy and Pathological Conditions. Pharm Res 2020; 37:137. [PMID: 32648115 PMCID: PMC7347686 DOI: 10.1007/s11095-020-2760-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/09/2020] [Indexed: 12/17/2022]
Abstract
PURPOSE We have developed a 3D brain unit network model to understand the spatial-temporal distribution of a drug within the brain under different (normal and disease) conditions. Our main aim is to study the impact of disease-induced changes in drug transport processes on spatial drug distribution within the brain extracellular fluid (ECF). METHODS The 3D brain unit network consists of multiple connected single 3D brain units in which the brain capillaries surround the brain ECF. The model includes the distribution of unbound drug within blood plasma, coupled with the distribution of drug within brain ECF and incorporates brain capillaryblood flow, passive paracellular and transcellular BBB transport, active BBB transport, brain ECF diffusion, brain ECF bulk flow, and specific and nonspecific brain tissue binding. All of these processes may change under disease conditions. RESULTS We show that the simulated disease-induced changes in brain tissue characteristics significantly affect drug concentrations within the brain ECF. CONCLUSIONS We demonstrate that the 3D brain unit network model is an excellent tool to gain understanding in the interdependencies of the factors governing spatial-temporal drug concentrations within the brain ECF. Additionally, the model helps in predicting the spatial-temporal brain ECF concentrations of existing drugs, under both normal and disease conditions.
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Affiliation(s)
- Esmée Vendel
- Mathematical Institute, Niels Bohrweg 1, 2333CA, Leiden, The Netherlands
| | - Vivi Rottschäfer
- Mathematical Institute, Niels Bohrweg 1, 2333CA, Leiden, The Netherlands.
| | - Elizabeth C M de Lange
- Leiden Academic Center for Drug Research, Einsteinweg 55, 2333CC, Leiden, The Netherlands.
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35
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Liu C, Xia L, Fu K, Cao X, Yan W, Cheng J, Roux T, Peletier LA, Yin X, Guo D. Revisit ligand-receptor interaction at the human vasopressin V 2 receptor: A kinetic perspective. Eur J Pharmacol 2020; 880:173157. [PMID: 32360346 DOI: 10.1016/j.ejphar.2020.173157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/07/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023]
Abstract
The vasopressin V2 receptor belongs to the superfamily of G protein-coupled receptors (GPCRs) and is a potential drug target for water balance disorders such as polycystic kidney disease. Traditionally, the discovery of novel agents for the vasopressin V2 receptor has been guided by evaluating their receptor affinity, largely ignoring the binding kinetics. However, the latter is receiving increasing attention in the drug research community and has been proved to be a more complete descriptor of the dynamic process of ligand-receptor interaction. Herein we aim to revisit the molecular basis of ligand-vasopressin V2 receptor interaction from the less-investigated kinetic perspective. A homogenous time-resolved fluorescence resonance energy transfer (TR-FRET) assay was set up and optimized, which enabled accurate kinetic profiling of unlabeled vasopressin V2 receptor ligands. Receptor occupancy profiles of two representative antagonists with distinct target residence time were simulated. Their functional effects were further explored in cAMP assays. Our results showed that the antagonist with longer receptor residence time (lixivaptan) displayed sustained target occupancy than the antagonist with shorter receptor residence time (mozavaptan). In accordance, lixivaptan displayed insurmountable antagonism and wash-resistant inhibitory effect on the cellular cAMP level, while not so for mozavaptan. Together, our data provide evidence that binding kinetics, next to their affinity, offers additional information for the dynamic process of ligand-receptor interaction. Hopefully, this study may lead to more kinetics-directed medicinal chemistry efforts and aid the design and discovery of different-in-class of vasopressin V2 receptor ligands for clinical applications.
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Affiliation(s)
- Chunji Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Leyi Xia
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Kequan Fu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Xudong Cao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China
| | - Wenzhong Yan
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Thomas Roux
- Cisbio Bioassays, Parc Marcel Boiteux, BP 84175, 30200, Codolet, France
| | - Lambertus A Peletier
- Mathematical Institute, Leiden University, P.O. Box 9512, 2300, RA, Leiden, the Netherlands
| | - Xiaoxing Yin
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
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36
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Wu N, Hammock BD, Lee KSS, An G. Simultaneous Target-Mediated Drug Disposition Model for Two Small-Molecule Compounds Competing for Their Pharmacological Target: Soluble Epoxide Hydrolase. J Pharmacol Exp Ther 2020; 374:223-232. [PMID: 32238455 DOI: 10.1124/jpet.120.265330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
1-(1-propanoylpiperidin-4-yl)-3-[4-(trifluoromethoxy)phenyl]urea (TPPU) and 1-(4-trifluoro-methoxy-phenyl)-3-(1-cyclopropanecarbonyl-piperidin-4-yl)-urea (TCPU) are potent inhibitors of soluble epoxide hydrolase (sEH) that have much better efficacy in relieving nociceptive response than the Food and Drug Administration-approved drug gabapentin in a rodent model of diabetic neuropathy. Experiments conducted in sEH knockout mice or with coadministration of a potent sEH displacer demonstrated that the pharmacokinetics of TPPU and TCPU were influenced by the specific binding to their pharmacologic target sEH, a phenomenon known as target-mediated drug disposition (TMDD). To quantitatively characterize the complex pharmacokinetics of TPPU and TCPU and gain better understanding on their target occupancy, population pharmacokinetics analysis using a nonlinear mixed-effect modeling approach was performed in the current study. The final model was a novel simultaneous TMDD interaction model, in which TPPU and TCPU compete for sEH, with TCPU binding to an additional unknown target pool with larger capacity that we refer to as a refractory pool. The total amount of sEH enzyme in mice was predicted to be 16.2 nmol, which is consistent with the experimental value of 10 nmol. The dissociate rate constants of TPPU and TCPU were predicted to be 2.24 and 2.67 hours-1, respectively, which is close to the values obtained from in vitro experiments. Our simulation result predicted that 90% of the sEH will be occupied shortly after a low dose of 0.3 mg/kg TPPU administration, with ≥40% of sEH remaining to be bound with TPPU for at least 7 days. Further efficacy experiments are warranted to confirm the predicted target occupancy. SIGNIFICANCE STATEMENT: Although target-mediated drug disposition (TMDD) models have been well documented, most of them were established in a single compound scenario. Our novel model represents the first TMDD interaction model for two small-molecule compounds competing for the same pharmacological target.
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Affiliation(s)
- Nan Wu
- Division of Pharmaceutics and Translational Therapeutics, College of Pharmacy, University of Iowa, Iowa city, Iowa (N.W., G.A.); Department of Entomology and Nematology and UCD Cancer Research Center, University of California at Davis, Davis, California (B.D.H.); and Departments of Pharmacology and Toxicology and Chemistry, Michigan State University, East Lansing, Michigan (K.S.S.L.)
| | - Bruce D Hammock
- Division of Pharmaceutics and Translational Therapeutics, College of Pharmacy, University of Iowa, Iowa city, Iowa (N.W., G.A.); Department of Entomology and Nematology and UCD Cancer Research Center, University of California at Davis, Davis, California (B.D.H.); and Departments of Pharmacology and Toxicology and Chemistry, Michigan State University, East Lansing, Michigan (K.S.S.L.)
| | - Kin Sing Stephen Lee
- Division of Pharmaceutics and Translational Therapeutics, College of Pharmacy, University of Iowa, Iowa city, Iowa (N.W., G.A.); Department of Entomology and Nematology and UCD Cancer Research Center, University of California at Davis, Davis, California (B.D.H.); and Departments of Pharmacology and Toxicology and Chemistry, Michigan State University, East Lansing, Michigan (K.S.S.L.)
| | - Guohua An
- Division of Pharmaceutics and Translational Therapeutics, College of Pharmacy, University of Iowa, Iowa city, Iowa (N.W., G.A.); Department of Entomology and Nematology and UCD Cancer Research Center, University of California at Davis, Davis, California (B.D.H.); and Departments of Pharmacology and Toxicology and Chemistry, Michigan State University, East Lansing, Michigan (K.S.S.L.)
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37
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van der Velden WJC, Heitman LH, Rosenkilde MM. Perspective: Implications of Ligand-Receptor Binding Kinetics for Therapeutic Targeting of G Protein-Coupled Receptors. ACS Pharmacol Transl Sci 2020; 3:179-189. [PMID: 32296761 DOI: 10.1021/acsptsci.0c00012] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Indexed: 12/16/2022]
Abstract
The concept of ligand-receptor binding kinetics has been broadly applied in drug development pipelines focusing on G protein-coupled receptors (GPCRs). The ligand residence time (RT) for a receptor describes how long a ligand-receptor complex exists, and is defined as the reciprocal of the dissociation rate constant (k off). RT has turned out to be a valuable parameter for GPCR researchers focusing on drug development as a good predictor of in vivo efficacy. The positive correlation between RT and in vivo efficacy has been established for several drugs targeting class A GPCRs (e.g., the neurokinin-1 receptor (NK1R), the β2 adrenergic receptor (β2AR), and the muscarinic 3 receptor (M3R)) and for drugs targeting class B1 (e.g., the glucagon-like peptide 1 receptor (GLP-1R)). Recently, the association rate constant (k on) has gained similar attention as another parameter affecting in vivo efficacy. In the current perspective, we address the importance of studying ligand-receptor binding kinetics for therapeutic targeting of GPCRs, with an emphasis on how binding kinetics can be altered by subtle molecular changes in the ligands and/or the receptors and how such changes affect treatment outcome. Moreover, we speculate on the impact of binding kinetic parameters for functional selectivity and sustained receptor signaling from endosomal compartments; phenomena that have gained increasing interest in attempts to improve therapeutic targeting of GPCRs.
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Affiliation(s)
- Wijnand J C van der Velden
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK 2200, Denmark
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Mette M Rosenkilde
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK 2200, Denmark
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38
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Vlachodimou A, Konstantinopoulou K, IJzerman AP, Heitman LH. Affinity, binding kinetics and functional characterization of draflazine analogues for human equilibrative nucleoside transporter 1 (SLC29A1). Biochem Pharmacol 2020; 172:113747. [DOI: 10.1016/j.bcp.2019.113747] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/05/2019] [Indexed: 12/31/2022]
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39
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The importance of target binding kinetics for measuring target binding affinity in drug discovery: a case study from a CRF1 receptor antagonist program. Drug Discov Today 2020; 25:7-14. [DOI: 10.1016/j.drudis.2019.09.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/16/2019] [Accepted: 09/13/2019] [Indexed: 12/28/2022]
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40
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Borisov DV, Veselovsky AV. [Ligand-receptor binding kinetics in drug design]. BIOMEDITSINSKAIA KHIMIIA 2020; 66:42-53. [PMID: 32116225 DOI: 10.18097/pbmc20206601042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Traditionally, the thermodynamic values of affinity are considered as the main criterion for the development of new drugs. Usually, these values for drugs are measured <i>in vitro</i> at steady concentrations of the receptor and ligand, which are differed from <i>in vivo</i> environment. Recent studies have shown that the kinetics of the process of drug binding to its receptor make significant contribution in the drug effectiveness. This has increased attention in characterizing and predicting the rate constants of association and dissociation of the receptor ligand at the stage of preclinical studies of drug candidates. A drug with a long residence time can determine ligand-receptor selectivity (kinetic selectivity), maintain pharmacological activity of the drug at its low concentration in vivo. The paper discusses the theoretical basis of protein-ligand binding, molecular determinants that control the kinetics of the drug-receptor binding. Understanding the molecular features underlying the kinetics of receptor-ligand binding will contribute to the rational design of drugs with desired properties.
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Affiliation(s)
- D V Borisov
- Institute of Biomedical Chemistry, Moscow, Russia
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41
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Fyfe TJ, Kellam B, Sykes DA, Capuano B, Scammells PJ, Lane JR, Charlton SJ, Mistry SN. Structure-Kinetic Profiling of Haloperidol Analogues at the Human Dopamine D 2 Receptor. J Med Chem 2019; 62:9488-9520. [PMID: 31580666 DOI: 10.1021/acs.jmedchem.9b00864] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Haloperidol is a typical antipsychotic drug (APD) associated with an increased risk of extrapyramidal side effects (EPSs) and hyperprolactinemia relative to atypical APDs such as clozapine. Both drugs are dopamine D2 receptor (D2R) antagonists, with contrasting kinetic profiles. Haloperidol displays fast association/slow dissociation at the D2R, whereas clozapine exhibits relatively slow association/fast dissociation. Recently, we have provided evidence that slow dissociation from the D2R predicts hyperprolactinemia, whereas fast association predicts EPS. Unfortunately, clozapine can cause severe side effects independent of its D2R action. Our results suggest an optimal kinetic profile for D2R antagonist APDs that avoids EPS. To begin exploring this hypothesis, we conducted a structure-kinetic relationship study of haloperidol and revealed that subtle structural modifications dramatically change binding kinetic rate constants, affording compounds with a clozapine-like kinetic profile. Thus, optimization of these kinetic parameters may allow development of novel APDs based on the haloperidol scaffold with improved side-effect profiles.
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Affiliation(s)
- Tim J Fyfe
- School of Pharmacy, Centre for Biomolecular Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Barrie Kellam
- School of Pharmacy, Centre for Biomolecular Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - David A Sykes
- School of Life Sciences, Queen's Medical Centre , University of Nottingham , Nottingham NG7 2UH , U.K.,Centre of Membrane Protein and Receptors , University of Nottingham , Nottingham NG7 2UH , U.K
| | | | | | - J Robert Lane
- School of Life Sciences, Queen's Medical Centre , University of Nottingham , Nottingham NG7 2UH , U.K.,Centre of Membrane Protein and Receptors , University of Nottingham , Nottingham NG7 2UH , U.K
| | - Steven J Charlton
- School of Life Sciences, Queen's Medical Centre , University of Nottingham , Nottingham NG7 2UH , U.K.,Centre of Membrane Protein and Receptors , University of Nottingham , Nottingham NG7 2UH , U.K.,Excellerate Bioscience Ltd., BioCity , Nottingham NG1 1GF , U.K
| | - Shailesh N Mistry
- School of Pharmacy, Centre for Biomolecular Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
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42
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Zhou Y, Zou R, Kuang G, Långström B, Halldin C, Ågren H, Tu Y. Enhanced Sampling Simulations of Ligand Unbinding Kinetics Controlled by Protein Conformational Changes. J Chem Inf Model 2019; 59:3910-3918. [DOI: 10.1021/acs.jcim.9b00523] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yang Zhou
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 10691, Sweden
| | - Rongfeng Zou
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 10691, Sweden
| | - Guanglin Kuang
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 10691, Sweden
| | - Bengt Långström
- Department of Chemistry, Uppsala University, Uppsala 75123, Sweden
| | - Christer Halldin
- Department of Clinical Neuroscience, Center for Psychiatric Research, Karolinska Institutet and Stockholm County Council, Stockholm 17176, Sweden
| | - Hans Ågren
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 10691, Sweden
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, P. R. China
| | - Yaoquan Tu
- Department of Theoretical Chemistry and Biology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 10691, Sweden
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43
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Babazada H, Alekberli T, Hajieva P, Farajov E. Biosensor-based kinetic and thermodynamic characterization of opioids interaction with human μ-opioid receptor. Eur J Pharm Sci 2019; 138:105017. [PMID: 31356868 DOI: 10.1016/j.ejps.2019.105017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/11/2019] [Accepted: 07/25/2019] [Indexed: 11/24/2022]
Abstract
Development of opioid analgesics with minimal side effects requires substantial knowledge on structure-kinetic and -thermodynamic relationship of opioid-receptor interactions. Here, combined kinetics and thermodynamics of opioid agonist binding to human μ-opioid receptor (h-μOR) was investigated using real-time label-free surface plasmon resonance (SPR)-based method. The N-terminal end truncated and C-terminal 6His-tagged h-μOR was constructed and expressed in E. coli. Receptor was purified, detergent-solubilized and characterized by circular dichroism. The uniform immobilization of h-μOR on Ni-NTA chips was achieved using hybrid capture-coupling approach followed by reconstitution in lipid bilayer. Thermodynamic equilibrium affinities of opioids were in narrow nanomolar range and in near quantitative agreement with their Ki values. However, they did not correlate with their in vitro EC50 values, indicating that they might not have thermodynamic selectivity. Contrary, on and off rates exhibited much larger dispersion and well correlated with EC50 values, indicating that opioids might exhibit kinetic-selectivity towards their target. Temperature-dependent SPR assays provided access to rate and equilibrium thermodynamic data, which demonstrated binding of morphine and naloxone to μOR was exothermic and essentially enthalpy driven. This work suggests that kinetic-based structure-activity of opioids in drug design and incorporation into the pharmacokinetics-pharmacodynamics predictions may have more value than thermodynamic equilibrium constants alone.
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Affiliation(s)
- Hasan Babazada
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshidaushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Tural Alekberli
- Department of Anesthesiology and Critical Care Medicine, Hadassah Medical Center, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | - Parvana Hajieva
- Cellular Adaptation Group, Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, 55128 Mainz, Germany
| | - Elnur Farajov
- Department of Internal Medicine, Azerbaijan Medical University, AZ1000 Baku, Azerbaijan.
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44
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Bosma R, Wang Z, Kooistra AJ, Bushby N, Kuhne S, van den Bor J, Waring MJ, de Graaf C, de Esch IJ, Vischer HF, Sheppard RJ, Wijtmans M, Leurs R. Route to Prolonged Residence Time at the Histamine H 1 Receptor: Growing from Desloratadine to Rupatadine. J Med Chem 2019; 62:6630-6644. [PMID: 31274307 PMCID: PMC6750840 DOI: 10.1021/acs.jmedchem.9b00447] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Drug–target
binding kinetics are an important predictor of in vivo drug efficacy,
yet the relationship
between ligand structures and their binding kinetics is often poorly
understood. We show that both rupatadine (1) and desloratadine
(2) have a long residence time at the histamine H1 receptor (H1R). Through development of a [3H]levocetirizine radiolabel, we find that the residence time
of 1 exceeds that of 2 more than 10-fold.
This was further explored with 22 synthesized rupatadine and desloratadine
analogues. Methylene-linked cycloaliphatic or β-branched substitutions
of desloratadine increase the residence time at the H1R,
conveying a longer duration of receptor antagonism. However, cycloaliphatic
substituents directly attached to the piperidine amine (i.e., lacking
the spacer) have decreased binding affinity and residence time compared
to their methylene-linked structural analogues. Guided by docking
studies, steric constraints within the binding pocket are hypothesized
to explain the observed differences in affinity and binding kinetics
between analogues.
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Affiliation(s)
- Reggie Bosma
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Zhiyong Wang
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Albert J Kooistra
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Nick Bushby
- Operations, BioPharmaceuticals R&D , AstraZeneca , Alderley Park , Macclesfield SK10 4TG , United Kingdom
| | - Sebastiaan Kuhne
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Jelle van den Bor
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Michael J Waring
- Medicinal Chemistry, Research and Early Development, Oncology R&D , AstraZeneca , Alderley Park , Macclesfield SK10 4TG , United Kingdom
| | - Chris de Graaf
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Iwan J de Esch
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Henry F Vischer
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Robert J Sheppard
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D , AstraZeneca , Gothenburg 431 50 , Sweden
| | - Maikel Wijtmans
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Rob Leurs
- Amsterdam Institute for Molecules, Medicines and Systems, Division of Medicinal Chemistry, Faculty of Science , VU University Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
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45
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Canal CE. Serotonergic Psychedelics: Experimental Approaches for Assessing Mechanisms of Action. Handb Exp Pharmacol 2019; 252:227-260. [PMID: 29532180 PMCID: PMC6136989 DOI: 10.1007/164_2018_107] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Recent, well-controlled - albeit small-scale - clinical trials show that serotonergic psychedelics, including psilocybin and lysergic acid diethylamide, possess great promise for treating psychiatric disorders, including treatment-resistant depression. Additionally, fresh results from a deluge of clinical neuroimaging studies are unveiling the dynamic effects of serotonergic psychedelics on functional activity within, and connectivity across, discrete neural systems. These observations have led to testable hypotheses regarding neural processing mechanisms that contribute to psychedelic effects and therapeutic benefits. Despite these advances and a plethora of preclinical and clinical observations supporting a central role for brain serotonin 5-HT2A receptors in producing serotonergic psychedelic effects, lingering and new questions about mechanisms abound. These chiefly pertain to molecular neuropharmacology. This chapter is devoted to illuminating and discussing such questions in the context of preclinical experimental approaches for studying mechanisms of action of serotonergic psychedelics, classic and new.
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Affiliation(s)
- Clinton E Canal
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University, Atlanta, GA, USA.
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46
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Vendel E, Rottschäfer V, de Lange ECM. The need for mathematical modelling of spatial drug distribution within the brain. Fluids Barriers CNS 2019; 16:12. [PMID: 31092261 PMCID: PMC6521438 DOI: 10.1186/s12987-019-0133-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/19/2019] [Indexed: 12/17/2022] Open
Abstract
The blood brain barrier (BBB) is the main barrier that separates the blood from the brain. Because of the BBB, the drug concentration-time profile in the brain may be substantially different from that in the blood. Within the brain, the drug is subject to distributional and elimination processes: diffusion, bulk flow of the brain extracellular fluid (ECF), extra-intracellular exchange, bulk flow of the cerebrospinal fluid (CSF), binding and metabolism. Drug effects are driven by the concentration of a drug at the site of its target and by drug-target interactions. Therefore, a quantitative understanding is needed of the distribution of a drug within the brain in order to predict its effect. Mathematical models can help in the understanding of drug distribution within the brain. The aim of this review is to provide a comprehensive overview of system-specific and drug-specific properties that affect the local distribution of drugs in the brain and of currently existing mathematical models that describe local drug distribution within the brain. Furthermore, we provide an overview on which processes have been addressed in these models and which have not. Altogether, we conclude that there is a need for a more comprehensive and integrated model that fills the current gaps in predicting the local drug distribution within the brain.
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Affiliation(s)
- Esmée Vendel
- Mathematical Institute, Leiden University, Niels Bohrweg 1, 2333CA, Leiden, The Netherlands
| | - Vivi Rottschäfer
- Mathematical Institute, Leiden University, Niels Bohrweg 1, 2333CA, Leiden, The Netherlands
| | - Elizabeth C M de Lange
- Leiden Academic Centre for Drug Research, Einsteinweg 55, 2333CC, Leiden, The Netherlands.
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47
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IJzerman AP, Guo D. Drug-Target Association Kinetics in Drug Discovery. Trends Biochem Sci 2019; 44:861-871. [PMID: 31101454 DOI: 10.1016/j.tibs.2019.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/28/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
Abstract
The important role of ligand-receptor binding kinetics in drug design and discovery is increasingly recognized by the drug research community. Over the past decade, accumulating evidence has shown that optimizing the ligand's dissociation rate constant can lead to desirable duration of in vivo target occupancy and, hence, improved pharmacodynamic properties. However, the association rate constant as a pharmacological principle remains less investigated, whereas it can play an equally important role in the selection of drug candidates. This review provides a compilation and discussion of otherwise scarce and dispersed information on this topic, bringing to light the importance of drug-target association in kinetics-directed drug design and discovery.
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Affiliation(s)
- Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300, RA, Leiden, The Netherlands
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
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48
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Li S, Qin C, Cui S, Xu H, Wu F, Wang J, Su M, Fang X, Li D, Jiao Q, Zhang M, Xia C, Zhu L, Wang R, Li J, Jiang H, Zhao Z, Li J, Li H. Discovery of a Natural-Product-Derived Preclinical Candidate for Once-Weekly Treatment of Type 2 Diabetes. J Med Chem 2019; 62:2348-2361. [PMID: 30694668 DOI: 10.1021/acs.jmedchem.8b01491] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Poor medication adherence is one of the leading causes of suboptimal glycaemic control in approximately half of the patients with type 2 diabetes mellitus (T2DM). Long-acting antidiabetic drugs are clinically needed for improving patients' compliance. Dipeptidyl peptidase-4 (DPP-4) inhibitors play an increasingly important role in the treatment of T2DM because of their favorable properties of weight neutrality and hypoglycemia avoidance. Herein, we report the successful discovery and scale-up synthesis of compound 5, a structurally novel, potent, and long-acting DPP-4 inhibitor for the once-weekly treatment of T2DM. Inhibitor 5 has fast-associating and slow-dissociating binding kinetics profiles as well as slow clearance rate and long terminal half-life pharmacokinetic properties. A single-dose oral administration of 5 (3 mg/kg) inhibited >80% of DPP-4 activity for more than 7 days in diabetic mice. The long-term antidiabetic efficacies of 5 (10 mg/kg, qw) were better than those of the once-weekly trelagliptin and omarigliptin, especially in decreasing the hemoglobin A1c level.
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Affiliation(s)
- Shiliang Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Chun Qin
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Shichao Cui
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , P. R. China
| | - Hongling Xu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Fangshu Wu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Jiawei Wang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Mingbo Su
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Xiaoyu Fang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Dan Li
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Qian Jiao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Ming Zhang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Chunmei Xia
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Rui Wang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Jia Li
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
| | - Jingya Li
- State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing 100049 , P. R. China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy , East China University of Science and Technology , Shanghai 200237 , China
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The implications of target saturation for the use of drug–target residence time. Nat Rev Drug Discov 2018; 18:82-84. [DOI: 10.1038/nrd.2018.234] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wang T, Rodina A, Dunphy MP, Corben A, Modi S, Guzman ML, Gewirth DT, Chiosis G. Chaperome heterogeneity and its implications for cancer study and treatment. J Biol Chem 2018; 294:2162-2179. [PMID: 30409908 DOI: 10.1074/jbc.rev118.002811] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The chaperome is the collection of proteins in the cell that carry out molecular chaperoning functions. Changes in the interaction strength between chaperome proteins lead to an assembly that is functionally and structurally distinct from each constituent member. In this review, we discuss the epichaperome, the cellular network that forms when the chaperome components of distinct chaperome machineries come together as stable, functionally integrated, multimeric complexes. In tumors, maintenance of the epichaperome network is vital for tumor survival, rendering them vulnerable to therapeutic interventions that target critical epichaperome network components. We discuss how the epichaperome empowers an approach for precision medicine cancer trials where a new target, biomarker, and relevant drug candidates can be correlated and integrated. We introduce chemical biology methods to investigate the heterogeneity of the chaperome in a given cellular context. Lastly, we discuss how ligand-protein binding kinetics are more appropriate than equilibrium binding parameters to characterize and unravel chaperome targeting in cancer and to gauge the selectivity of ligands for specific tumor-associated chaperome pools.
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Affiliation(s)
- Tai Wang
- From the Chemical Biology Program and
| | | | | | - Adriana Corben
- the Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Shanu Modi
- Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Monica L Guzman
- Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, and
| | - Daniel T Gewirth
- the Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203
| | - Gabriela Chiosis
- From the Chemical Biology Program and .,Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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