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Davel CM, Bernat T, Wagner JR, Shirts MR. Parameterization of General Organic Polymers within the Open Force Field Framework. J Chem Inf Model 2024; 64:1290-1305. [PMID: 38303159 PMCID: PMC11090695 DOI: 10.1021/acs.jcim.3c01691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Polymer and chemically modified biopolymer systems present unique challenges to traditional molecular simulation preparation workflows. First, typical polymer and biomolecular input formats, such as Protein Data Bank (PDB) files, lack adequate chemical information needed for the parameterization of new chemistries. Second, polymers are typically too large for accurate partial charge generation methods. In this work, we employ direct chemical perception through the Open Force Field toolkit to create a flexible polymer simulation workflow for organic polymers, encompassing everything from biopolymers to soft materials. We propose and test a new input specification for monomer information that can, along with a 3D conformational geometry, parametrize and simulate most soft-material systems within the same workflow used for smaller ligands. The monomer format encompasses a subset of the SMIRKS substructure query language to uniquely identify chemical information and repeating charges in underspecified systems through matching atomic connectivity. This workflow is combined with several different approaches for automatic partial-charge generation for larger systems. As an initial proof of concept, a variety of diverse polymeric systems were parametrized with the Open Force Field toolkit, including functionalized proteins, DNA, homopolymers, cross-linked systems, and sugars. Additionally, shape properties and radial distribution functions were computed from molecular dynamics simulations of poly(ethylene glycol), polyacrylamide, and poly(N-isopropylacrylamide) homopolymers in aqueous solution and compared to previous simulation results in order to demonstrate a start-to-finish workflow for simulation and property prediction. We expect that these tools will greatly expedite the day-to-day computational research of soft-matter simulations and create a robust atomic-scale polymer specification in conjunction with existing polymer structural notations.
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Affiliation(s)
- Connor M Davel
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Timotej Bernat
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Jeffrey R Wagner
- The Open Force Field Initiative, Open Molecular Software Foundation, Davis, California 95616, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
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2
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Dewaker V, Sharma AR, Debnath U, Park ST, Kim HS. Insights from molecular dynamics simulations of TRPV1 channel modulators in pain. Drug Discov Today 2023; 28:103798. [PMID: 37838068 DOI: 10.1016/j.drudis.2023.103798] [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: 07/28/2023] [Revised: 09/28/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023]
Abstract
TRPV1 is a nonselective cation channel vital for detecting noxious stimuli (heat, acid, capsaicin). Its role in pain makes it a potential drug target for chronic pain management, migraines, and related disorders. This review updates molecular dynamics (MD) simulation studies on the TRPV1 channel, focusing on its gating mechanism, ligand-binding sites, and implications for drug design. The article also explores challenges in developing modulators, SAR optimization, and clinical trial studies. Efforts have been undertaken to concisely present MD simulation findings, with a focus on their relevance to drug discovery.
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Affiliation(s)
- Varun Dewaker
- Institute of New Frontier Research Team, Hallym University, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Ashish R Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si 24252, Gangwon-do, Republic of Korea
| | - Utsab Debnath
- School of Health Sciences & Technology, UPES, Dehradun, Uttarakhand 248007, India
| | - Sung Taek Park
- Institute of New Frontier Research Team, Hallym University, Chuncheon-si 24252, Gangwon-do, Republic of Korea; Department of Obstetrics and Gynecology, Kangnam Sacred-Heart Hospital, Hallym University Medical Center, Hallym University College of Medicine, Seoul 07441, Republic of Korea; EIONCELL Inc., Chuncheon 24252, Republic of Korea
| | - Hyeong Su Kim
- Institute of New Frontier Research Team, Hallym University, Chuncheon-si 24252, Gangwon-do, Republic of Korea; Division of Hemato-Oncology, Department of Internal Medicine, Kangnam Sacred-Heart Hospital, Hallym University Medical Center, Hallym University College of Medicine, Seoul 07441, Republic of Korea; EIONCELL Inc., Chuncheon 24252, Republic of Korea.
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3
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Tuo Y, Tang Y, Yu Y, Luo M, Liang H, Wang Y. Structural optimization and binding energy prediction for globomycin analogs based on 3D-QSAR and molecular simulations. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.134981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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4
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Dong L, Zhou Q, Liang Q, Qiao Z, Liu Y, Shao L, Wang K. Identification of a Partial and Selective TRPV1 Agonist CPIPC for Alleviation of Inflammatory Pain. Molecules 2022; 27:molecules27175428. [PMID: 36080196 PMCID: PMC9457966 DOI: 10.3390/molecules27175428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Transient receptor potential vanilloid 1 (TRPV1) is a non-selective cation channel, predominantly expressed in a subset of peripheral sensory neurons for pain signaling. Topical application of agonist capsaicin for desensitizing TRPV1 currents has been approved for relief of chronic pain. However, the potent TRPV1 capsaicin is not ingestible and even topical capsaicin causes common side effects such as skin irritation, swelling, erythema and pruritus, suggesting that a mild TRPV1 agonist might be helpful for reducing side effects while reliving pain. In this study, we reported on a partial and selective TRPV1 agonist 4-(5-chloropyridin-2-yl)-N-(1H-indazol-6-yl)piperazine-1-carboxamide named CPIPC that was modified based on targeting the residue Arg557, important for conversion between the channel antagonism and agonism. Whole-cell patch clamp recordings indicated a concentration-dependent activation of TRPV1 currents by CPIPC with an EC50 of 1.56 ± 0.13 μM. The maximum efficacy of CPIPC (30 μM) was about 60% of saturated capsaicin (10 μM). Repetitive additions of CPIPC caused TRPV1 current desensitization in both TRPV1-expressing HEK293 cells and dorsal root ganglion (DRG) sensory neurons. Oral administration of CPIPC dose-dependently alleviated inflammatory pain in mice. Further site-directed mutagenesis combined with molecular docking revealed that residue Arg557 is critical for TRPV1 activation by CPIPC. Taken together, we identified a novel partial and selective TRPV1 agonist CPIPC that exhibits antinociceptive activity in mice.
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Affiliation(s)
- Liying Dong
- Departments of Pharmacology, School of Pharmacy, Qingdao University Medical College, Qingdao 266073, China
| | - Qiqi Zhou
- Department of Pharmacology, Qilu Medical University, Zibo 255300, China
| | - Qianqian Liang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, No. 826 Zhangheng Road, Shanghai 201203, China
| | - Zhen Qiao
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, No. 826 Zhangheng Road, Shanghai 201203, China
| | - Yani Liu
- Departments of Pharmacology, School of Pharmacy, Qingdao University Medical College, Qingdao 266073, China
- Institute of Innovative Drug Discovery, Qingdao University Medical College, 38 Dengzhou Road, Qingdao 266021, China
- Correspondence: (Y.L.); (L.S.); (K.W.)
| | - Liming Shao
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, No. 826 Zhangheng Road, Shanghai 201203, China
- Correspondence: (Y.L.); (L.S.); (K.W.)
| | - Kewei Wang
- Departments of Pharmacology, School of Pharmacy, Qingdao University Medical College, Qingdao 266073, China
- Institute of Innovative Drug Discovery, Qingdao University Medical College, 38 Dengzhou Road, Qingdao 266021, China
- Correspondence: (Y.L.); (L.S.); (K.W.)
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5
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Liang Q, Qiao Z, Zhou Q, Xue D, Wang K, Shao L. Discovery of Potent and Selective Transient Receptor Potential Vanilloid 1 (TRPV1) Agonists with Analgesic Effects In Vivo Based on the Functional Conversion Induced by Altering the Orientation of the Indazole Core. J Med Chem 2022; 65:11658-11678. [PMID: 36008373 DOI: 10.1021/acs.jmedchem.2c00469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Transient receptor potential vanilloid 1 (TRPV1) is a promising target for developing antinociceptive agents. Here, we report the synthesis of N-indazole-4-aryl piperazine carboxamide analogues as TRPV1 modulators. The structure-activity relationship (SAR) reveals that substituting indazole at the 5-/6-position leads to TRPV1 agonism, whereas the 4- and 7-positions of indazole obtain mild antagonism and loss of activity, respectively. The whole-cell clamp patch assay shows that 28 is a potent and selective TRPV1 agonist and it relieves inflammatory and thermal pain by desensitizing the native TRPV1 current in the dorsal root ganglion (DRG) in mice. Additionally, site-directed mutagenesis combined with molecular docking shows an important hydrogen interaction between Arg557 and the indazole of 28. Taken together, our findings provide insight into TRPV1 agonism-antagonism conversion based on the interaction between indazole and Arg557, which provides a strategy to obtain new TRPV1 agonists by structural modification of antagonists. Compound 28 may be used as a lead compound for further optimization.
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Affiliation(s)
- Qianqian Liang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Zhen Qiao
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Qiqi Zhou
- Department of Pharmacology, Qilu Medical University, Zibo, Shandong 255300, China
| | - Dengqi Xue
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.,State Key Laboratory of Medical Neurobiology, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
| | - KeWei Wang
- Departments of Pharmacology, School of Pharmacy, Qingdao University Medical College, #1 Ningde Road, Qingdao 266073, China.,Institute of Innovative Drug Discovery, Qingdao University, 38 Dengzhou Road, Qingdao 266021, China
| | - Liming Shao
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.,State Key Laboratory of Medical Neurobiology, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
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6
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He Q, Zhao L, Li G, Shen Y, Hu Y, Wang Y. The antimicrobial cyclic peptide B2 combats multidrug resistant Acinetobacter baumannii infection. NEW J CHEM 2022. [DOI: 10.1039/d1nj05353a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In silico methods were employed for the development of antimicrobial peptides against MDR A. baumannii by binding to BamA.
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Affiliation(s)
- Qingxiu He
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Linan Zhao
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Guangping Li
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Yan Shen
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
- Chongqing Key Laboratory of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing, China, 400054
- Chongqing Key Laboratory of Target Based Drug Screening and Activity Evaluation, Chongqing University of Technology, Chongqing, China, 400054
| | - Yong Hu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
- Chongqing Key Laboratory of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing, China, 400054
- Chongqing Key Laboratory of Target Based Drug Screening and Activity Evaluation, Chongqing University of Technology, Chongqing, China, 400054
| | - Yuanqiang Wang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
- Chongqing Key Laboratory of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing, China, 400054
- Chongqing Key Laboratory of Target Based Drug Screening and Activity Evaluation, Chongqing University of Technology, Chongqing, China, 400054
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China, 400716
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Luu DD, Owens AM, Mebrat MD, Van Horn WD. A molecular perspective on identifying TRPV1 thermosensitive regions and disentangling polymodal activation. Temperature (Austin) 2021; 10:67-101. [PMID: 37187836 PMCID: PMC10177694 DOI: 10.1080/23328940.2021.1983354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022] Open
Abstract
TRPV1 is a polymodal receptor ion channel that is best known to function as a molecular thermometer. It is activated in diverse ways, including by heat, protons (low pH), and vanilloid compounds, such as capsaicin. In this review, we summarize molecular studies of TRPV1 thermosensing, focusing on the cross-talk between heat and other activation modes. Additional insights from TRPV1 isoforms and non-rodent/non-human TRPV1 ortholog studies are also discussed in this context. While the molecular mechanism of heat activation is still emerging, it is clear that TRPV1 thermosensing is modulated allosterically, i.e., at a distance, with contributions from many distinct regions of the channel. Similarly, current studies identify cross-talk between heat and other TRPV1 activation modes, such as protons and capsaicin, and that these modes can generally be selectively disentangled. In aggregate, this suggests that future TRPV1 molecular studies should define allosteric pathways and provide mechanistic insight, thereby enabling mode-selective manipulation of the polymodal receptor. These advances are anticipated to have significant implications in both basic and applied biomedical sciences.
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Affiliation(s)
- Dustin D. Luu
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- The Biodesign Institute Virginia G. Piper Center for Personalized Diagnostics,Arizona State University, Tempe, Arizona,USA
| | - Aerial M. Owens
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- The Biodesign Institute Virginia G. Piper Center for Personalized Diagnostics,Arizona State University, Tempe, Arizona,USA
| | - Mubark D. Mebrat
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- The Biodesign Institute Virginia G. Piper Center for Personalized Diagnostics,Arizona State University, Tempe, Arizona,USA
| | - Wade D. Van Horn
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- The Biodesign Institute Virginia G. Piper Center for Personalized Diagnostics,Arizona State University, Tempe, Arizona,USA
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8
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Li G, Guo H, Zhao L, Feng H, He H, Chen Y, Wang Y, Lin Z. Discovery of modulators for the PD-1/PD-L1 interaction by molecular simulation and bioassay. NEW J CHEM 2021. [DOI: 10.1039/d1nj02030g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
PD-1-targeted discovery of modulators by virtual screening, molecular docking, surface plasmon resonance binding assay and T-cell activation assay.
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Affiliation(s)
- Guangping Li
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Haiqiong Guo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Linan Zhao
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Huixian Feng
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510005, China
| | - Huawei He
- Biological Science Research Center, Southwest University, Chongqing, 400716, China
| | - Yan Chen
- College of Pharmacology Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yuanqiang Wang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
- Chongqing Key Laboratory of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing, 400054, China
- Key Laboratory of Target Based Drug Screening and Activity Evaluation, Chongqing University of Technology, Chongqing, 400054, China
| | - Zhihua Lin
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
- Chongqing Key Laboratory of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing, 400054, China
- Key Laboratory of Target Based Drug Screening and Activity Evaluation, Chongqing University of Technology, Chongqing, 400054, China
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9
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Abstract
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.
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Ali B, Jamal QMS, Mir SR, Shams S, Kamal MA. Molecular docking studies of tea ( Thea sinensis Linn.) polyphenols inhibition pattern with Rat P-glycoprotein. PHYSICAL SCIENCES REVIEWS 2020. [DOI: 10.1515/psr-2018-0165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Abstract
Since 3000 B.C., evergreen plant Thea sinensis (Theaceae) is used both as a social and medicinal beverage. Leaves of T. sinensis contain amino acids, vitamins, caffeine, polysaccharides and polyphenols. Most of the natural medicinal actions of tea are due to the availability and abundance of polyphenols mainly catechins. It has also been stated that some catechins were absorbed more rapidly than other compounds after the oral administration of tea and could increase the bio-enhancing activities of anticancer drugs by inhibiting P-glycoprotein (P-gp). The results of the molecular docking showed that polyphenols bind easily to the active P-gp site. All compounds exhibited fluctuating binding affinity ranged from −11.67 to −8.36 kcal/mol. Observed binding energy required for theaflavin to bind to P-gp was lowest (−11.67 kcal/mol). The obtained data that supports all the selected polyphenols inhibited P-gp and therefore may enhance the bioavailability of drugs. This study may play a vital role in finding hotspots in P-gp and eventually may be proved useful in designing compounds with high affinity and specificity to the protein.
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Affiliation(s)
- Babar Ali
- College of Pharmacy and Dentistry , Buraydah Colleges , Buraydah , Al-Qassim , Kingdom of Saudi Arabia
| | - Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics , Qassim University , Al Bukayriyah , Saudi Arabia
- Novel Global Community Educational Foundation , Hebersham , Australia
| | - Showkat R. Mir
- Department of Pharmacognosy and Phytochemistry , Faculty of Pharmacy, Jamia Hamdard (Hamdard University) , New Delhi 110062 , India
| | - Saiba Shams
- Siddhartha Institute of Pharmacy , Dehra Dun 248001 , Uttarakhand , India
| | - Mohammad Amjad Kamal
- King Fahd Medical Research Center , King Abdulaziz University , Jeddah , Saudi Arabia
- West China School of Nursing / Institutes for Systems Genetics , Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University , Chengdu 610041 , Sichuan , China
- Enzymoics, 7 Peterlee Place , Hebersham , NSW 2770, Novel Global Community Educational Foundation , Australia
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11
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Chu Y, Cohen BE, Chuang HH. A single TRPV1 amino acid controls species sensitivity to capsaicin. Sci Rep 2020; 10:8038. [PMID: 32415171 PMCID: PMC7229161 DOI: 10.1038/s41598-020-64584-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/11/2020] [Indexed: 11/09/2022] Open
Abstract
Chili peppers produce capsaicin (a vanilloid) that activates the transient receptor potential cation channel subfamily V member 1 (TRPV1) on sensory neurons to alter their membrane potential and induce pain. To identify residues responsible for differential TRPV1 capsaicin sensitivity among species, we used intracellular Ca2+ imaging to characterize chimeras composed of capsaicin-sensitive rat TRPV1 (rTRPV1) and capsaicin-insensitive chicken TRPV1 (cTRPV1) exposed to a series of capsaicinoids. We found that chimeras containing rat E570-V686 swapped into chicken receptors displayed capsaicin sensitivity, and that simply changing the alanine at position 578 in the S4-S5 helix of the chicken receptor to a glutamic acid was sufficient to endow it with capsaicin sensitivity in the micromolar range. Moreover, introduction of lysine, glutamine or proline at residue A578 also elicited capsaicin sensitivity in cTRPV1. Similarly, replacing corresponding rTRPV1 residue E570 with lysine or glutamine retained capsaicin sensitivity. The hydrophilic capsaicin analog Cap-EA activated a cTRPV1-A578E mutant, suggesting that A578 may participate in vanilloid binding. The hydrophilic vanilloid agonist zingerone did not activate any A578 mutants with capsaicin sensitivity, suggesting that the vanilloid group alone is not sufficient for receptor activation. Our study demonstrates that a subtle modification of TRPV1 in different species globally alters capsaicin responses.
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Affiliation(s)
- Ying Chu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.
| | - Bruce E Cohen
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Huai-Hu Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
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12
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Journigan VB, Feng Z, Rahman S, Wang Y, Amin ARMR, Heffner CE, Bachtel N, Wang S, Gonzalez-Rodriguez S, Fernández-Carvajal A, Fernández-Ballester G, Hilton JK, Van Horn WD, Ferrer-Montiel A, Xie XQ, Rahman T. Structure-Based Design of Novel Biphenyl Amide Antagonists of Human Transient Receptor Potential Cation Channel Subfamily M Member 8 Channels with Potential Implications in the Treatment of Sensory Neuropathies. ACS Chem Neurosci 2020; 11:268-290. [PMID: 31850745 DOI: 10.1021/acschemneuro.9b00404] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Structure-activity relationship studies of a reported menthol-based transient receptor potential cation channel subfamily M member 8 channel (TRPM8) antagonist, guided by computational simulations and structure-based design, uncovers a novel series of TRPM8 antagonists with >10-fold selectivity versus related TRP subtypes. Spiro[4.5]decan-8-yl analogue 14 inhibits icilin-evoked Ca2+ entry in HEK-293 cells stably expressing human TRPM8 (hTRPM8) with an IC50 of 2.4 ± 1.0 nM, while in whole-cell patch-clamp recordings this analogue inhibits menthol-evoked currents with a hTRPM8 IC50 of 64 ± 2 nM. Molecular dynamics (MD) simulations of compound 14 in our homology model of hTRPM8 suggest that this antagonist forms extensive hydrophobic contacts within the orthosteric site. In the wet dog shakes (WDS) assay, compound 14 dose-dependently blocks icilin-triggered shaking behaviors in mice. Upon local administration, compound 14 dose dependently inhibits cold allodynia evoked by the chemotherapy oxaliplatin in a murine model of peripheral neuropathy at microgram doses. Our findings suggest that 14 and other biphenyl amide analogues within our series can find utility as potent antagonist chemical probes derived from (-)-menthol as well as small molecule therapeutic scaffolds for chemotherapy-induced peripheral neuropathy (CIPN) and other sensory neuropathies.
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Affiliation(s)
- V. Blair Journigan
- Department of Pharmaceutical Sciences, School of Pharmacy, Marshall University, Huntington, West Virginia 25755, United States
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia 25755, United States
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Saifur Rahman
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1TN, United Kingdom
| | - Yuanqiang Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - A. R. M. Ruhul Amin
- Department of Pharmaceutical Sciences, School of Pharmacy, Marshall University, Huntington, West Virginia 25755, United States
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia 25755, United States
| | - Colleen E. Heffner
- Department of Pharmaceutical Sciences, School of Pharmacy, Marshall University, Huntington, West Virginia 25755, United States
| | - Nicholas Bachtel
- Department of Pharmaceutical Sciences, School of Pharmacy, Marshall University, Huntington, West Virginia 25755, United States
| | - Siyi Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Sara Gonzalez-Rodriguez
- IDiBE: Instituto de Investigación, Desarrollo e innovación en Biotecnología sanitaria de Elche, Universitas Miguel Hernández, 03202 Elche, Spain
| | - Asia Fernández-Carvajal
- IDiBE: Instituto de Investigación, Desarrollo e innovación en Biotecnología sanitaria de Elche, Universitas Miguel Hernández, 03202 Elche, Spain
| | - Gregorio Fernández-Ballester
- IDiBE: Instituto de Investigación, Desarrollo e innovación en Biotecnología sanitaria de Elche, Universitas Miguel Hernández, 03202 Elche, Spain
| | - Jacob K. Hilton
- The School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- the Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
- The Magnetic Resonance Research Center, Arizona State University, Tempe, Arizona 85287, United States
| | - Wade D. Van Horn
- The School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- the Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
- The Magnetic Resonance Research Center, Arizona State University, Tempe, Arizona 85287, United States
| | - Antonio Ferrer-Montiel
- IDiBE: Instituto de Investigación, Desarrollo e innovación en Biotecnología sanitaria de Elche, Universitas Miguel Hernández, 03202 Elche, Spain
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Taufiq Rahman
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1TN, United Kingdom
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Xing C, Zhuang Y, Xu TH, Feng Z, Zhou XE, Chen M, Wang L, Meng X, Xue Y, Wang J, Liu H, McGuire TF, Zhao G, Melcher K, Zhang C, Xu HE, Xie XQ. Cryo-EM Structure of the Human Cannabinoid Receptor CB2-G i Signaling Complex. Cell 2020; 180:645-654.e13. [PMID: 32004460 DOI: 10.1016/j.cell.2020.01.007] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/01/2019] [Accepted: 01/06/2020] [Indexed: 02/08/2023]
Abstract
Drugs selectively targeting CB2 hold promise for treating neurodegenerative disorders, inflammation, and pain while avoiding psychotropic side effects mediated by CB1. The mechanisms underlying CB2 activation and signaling are poorly understood but critical for drug design. Here we report the cryo-EM structure of the human CB2-Gi signaling complex bound to the agonist WIN 55,212-2. The 3D structure reveals the binding mode of WIN 55,212-2 and structural determinants for distinguishing CB2 agonists from antagonists, which are supported by a pair of rationally designed agonist and antagonist. Further structural analyses with computational docking results uncover the differences between CB2 and CB1 in receptor activation, ligand recognition, and Gi coupling. These findings are expected to facilitate rational structure-based discovery of drugs targeting the cannabinoid system.
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Affiliation(s)
- Changrui Xing
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screen Center, School of Pharmacy, and NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA; Drug Discovery Institute and Departments of Computational Biology and of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Youwen Zhuang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China; Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ting-Hai Xu
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screen Center, School of Pharmacy, and NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA; Drug Discovery Institute and Departments of Computational Biology and of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - X Edward Zhou
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Maozi Chen
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screen Center, School of Pharmacy, and NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Lei Wang
- Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Xing Meng
- David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Ying Xue
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screen Center, School of Pharmacy, and NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Pharmacy and Therapeutics, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screen Center, School of Pharmacy, and NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Heng Liu
- Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Terence Francis McGuire
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screen Center, School of Pharmacy, and NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Gongpu Zhao
- David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Karsten Melcher
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Cheng Zhang
- Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - H Eric Xu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences, Computational Chemical Genomics Screen Center, School of Pharmacy, and NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA; Drug Discovery Institute and Departments of Computational Biology and of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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14
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Chahal V, Nirwan S, Kakkar R. Combined approach of homology modeling, molecular dynamics, and docking: computer-aided drug discovery. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2019-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
With the continuous development in software, algorithms, and increase in computer speed, the field of computer-aided drug design has been witnessing reduction in the time and cost of the drug designing process. Structure based drug design (SBDD), which is based on the 3D structure of the enzyme, is helping in proposing novel inhibitors. Although a number of crystal structures are available in various repositories, there are various proteins whose experimental crystallization is difficult. In such cases, homology modeling, along with the combined application of MD and docking, helps in establishing a reliable 3D structure that can be used for SBDD. In this review, we have reported recent works, which have employed these three techniques for generating structures and further proposing novel inhibitors, for cytoplasmic proteins, membrane proteins, and metal containing proteins. Also, we have discussed these techniques in brief in terms of the theory involved and the various software employed. Hence, this review can give a brief idea about using these tools specifically for a particular problem.
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15
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Wang Y, Guo H, Feng Z, Wang S, Wang Y, He Q, Li G, Lin W, Xie XQ, Lin Z. PD-1-Targeted Discovery of Peptide Inhibitors by Virtual Screening, Molecular Dynamics Simulation, and Surface Plasmon Resonance. Molecules 2019; 24:molecules24203784. [PMID: 31640203 PMCID: PMC6833008 DOI: 10.3390/molecules24203784] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 11/16/2022] Open
Abstract
The blockade of the programmed cell death protein 1/programmed cell death ligand 1 (PD-1/PD-L1) pathway plays a critical role in cancer immunotherapy by reducing the immune escape. Five monoclonal antibodies that antagonized PD-1/PD-L1 interaction have been approved by the Food and Drug Administration (FDA) and marketed as immunotherapy for cancer treatment. However, some weaknesses of antibodies, such as high cost, low stability, poor amenability for oral administration, and immunogenicity, should not be overlooked. To overcome these disadvantages, small-molecule inhibitors targeting PD-L1 were developed. In the present work, we applied in silico and in vitro approaches to develop short peptides targeting PD-1 as chemical probes for the inhibition of PD-1-PD-L1 interaction. We first predicted the potential binding pocket on PD-1/PD-L1 protein-protein interface (PPI). Sequentially, we carried out virtual screening against our in-house peptide library to identify potential ligands. WANG-003, WANG-004, and WANG-005, three of our in-house peptides, were predicted to bind to PD-1 with promising docking scores. Next, we conducted molecular docking and molecular dynamics (MD) simulation for the further analysis of interactions between our peptides and PD-1. Finally, we evaluated the affinity between peptides and PD-1 by surface plasmon resonance (SPR) binding technology. The present study provides a new perspective for the development of PD-1 inhibitors that disrupt PD-1-PD-L1 interactions. These promising peptides have the potential to be utilized as a novel chemical probe for further studies, as well as providing a foundation for further designs of potent small-molecule inhibitors targeting PD-1.
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Affiliation(s)
- Yuanqiang Wang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing 400054, China.
- Chongqing Key Laboratory of Target Based Drug Screening and Effect Evaluation, Chongqing 400054, China.
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China.
| | - Haiqiong Guo
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing 400054, China.
- Chongqing Key Laboratory of Target Based Drug Screening and Effect Evaluation, Chongqing 400054, China.
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA.
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Siyi Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA.
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Yuxuan Wang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing 400054, China.
- Chongqing Key Laboratory of Target Based Drug Screening and Effect Evaluation, Chongqing 400054, China.
| | - Qingxiu He
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing 400054, China.
- Chongqing Key Laboratory of Target Based Drug Screening and Effect Evaluation, Chongqing 400054, China.
| | - Guangping Li
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing 400054, China.
- Chongqing Key Laboratory of Target Based Drug Screening and Effect Evaluation, Chongqing 400054, China.
| | - Weiwei Lin
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA.
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA.
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA 15261, USA.
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA.
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Zhihua Lin
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing 400054, China.
- Chongqing Key Laboratory of Target Based Drug Screening and Effect Evaluation, Chongqing 400054, China.
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16
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Wang L, Liu M, Yin F, Wang Y, Li X, Wu Y, Ye C, Liu J. Trilobatin, a Novel SGLT1/2 Inhibitor, Selectively Induces the Proliferation of Human Hepatoblastoma Cells. Molecules 2019; 24:molecules24183390. [PMID: 31540429 PMCID: PMC6767144 DOI: 10.3390/molecules24183390] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/11/2019] [Accepted: 09/14/2019] [Indexed: 02/08/2023] Open
Abstract
Studies have indicated that Na+-d-glucose co-transporter (SGLT) inhibitors had anti-proliferative activity by attenuating the uptake of glucose in several tumor cell lines. In this study, the molecular docking showed that, trilobatin, one of the dihydrochalcones from leaves of Lithocarpus polystachyus Rehd., might be a novel inhibitor of SGLT1 and SGLT2, which evidently attenuated the uptake of glucose in vitro and in vivo. To our surprise, we observed that trilobatin did not inhibit, but promoted the proliferation of human hepatoblastoma HepG2 and Huh 7 cells when it was present at high concentrations. At the same time, incubation with high concentrations of trilobatin arrested the cell cycle at S phase in HepG2 cells. We also found that treatment with trilobatin had no significant effect on the expression of hepatitis B x-interacting protein (HBXIP) and hepatocyte nuclear factor (HNF)-4α, the two key regulators of hepatocyte proliferation. Taken together, although trilobatin worked as a novel inhibitor of SGLTs to attenuate the uptake of glucose, it also selectively induced the cell proliferation of HepG2 cells, suggesting that not all the SGLT inhibitors inhibited the proliferation of tumor cells, and further studies are needed to assess the anti-cancer potentials of new glucose-lowering agents.
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Affiliation(s)
- Lujing Wang
- Chongqing Key Lab of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China.
| | - Min Liu
- Chongqing Key Lab of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China.
| | - Fei Yin
- Chongqing Key Lab of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China.
| | - Yuanqiang Wang
- Chongqing Key Lab of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China.
| | - Xingan Li
- Chongqing Key Lab of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China.
| | - Yucui Wu
- Chongqing Key Lab of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China.
| | - Cuilian Ye
- Chongqing Key Lab of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China.
| | - Jianhui Liu
- Chongqing Key Lab of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China.
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17
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Torres PHM, Sodero ACR, Jofily P, Silva-Jr FP. Key Topics in Molecular Docking for Drug Design. Int J Mol Sci 2019; 20:E4574. [PMID: 31540192 PMCID: PMC6769580 DOI: 10.3390/ijms20184574] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/18/2022] Open
Abstract
Molecular docking has been widely employed as a fast and inexpensive technique in the past decades, both in academic and industrial settings. Although this discipline has now had enough time to consolidate, many aspects remain challenging and there is still not a straightforward and accurate route to readily pinpoint true ligands among a set of molecules, nor to identify with precision the correct ligand conformation within the binding pocket of a given target molecule. Nevertheless, new approaches continue to be developed and the volume of published works grows at a rapid pace. In this review, we present an overview of the method and attempt to summarise recent developments regarding four main aspects of molecular docking approaches: (i) the available benchmarking sets, highlighting their advantages and caveats, (ii) the advances in consensus methods, (iii) recent algorithms and applications using fragment-based approaches, and (iv) the use of machine learning algorithms in molecular docking. These recent developments incrementally contribute to an increase in accuracy and are expected, given time, and together with advances in computing power and hardware capability, to eventually accomplish the full potential of this area.
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Affiliation(s)
- Pedro H M Torres
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
| | - Ana C R Sodero
- Department of Drugs and Medicines; School of Pharmacy; Federal University of Rio de Janeiro, Rio de Janeiro 21949-900, RJ, Brazil.
| | - Paula Jofily
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21949-900, RJ, Brazil.
| | - Floriano P Silva-Jr
- Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21949-900, RJ, Brazil.
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18
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Pearce LV, Ann J, Blumberg PM, Lee J. Combination of a Rapidly Penetrating Agonist and a Slowly Penetrating Antagonist Affords Agonist Action of Limited Duration at the Cellular Level. Biomol Ther (Seoul) 2019; 27:435-441. [PMID: 31302951 PMCID: PMC6720535 DOI: 10.4062/biomolther.2019.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 11/21/2022] Open
Abstract
The capsaicin receptor TRPV1 (transient receptor potential vanilloid 1) has been an object of intense interest for pharmacological development on account of its critical role in nociception. In the course of structure activity analysis, it has become apparent that TRPV1 ligands may vary dramatically in the rates at which they interact with TRPV1, presumably reflecting differences in their abilities to penetrate into the cell. Using a fast penetrating agonist together with an excess of a slower penetrating antagonist, we find that we can induce an agonist response of limited duration and, moreover, the duration of the agonist response remains largely independent of the absolute dose of agonist, as long as the ratio of antagonist to agonist is held constant. This general approach for limiting agonist duration under conditions in which absolute agonist dose is variable should have more general applicability.
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Affiliation(s)
- Larry V Pearce
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-4255, USA
| | - Jihyae Ann
- Laboratory of Medicinal Chemistry, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Peter M Blumberg
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-4255, USA
| | - Jeewoo Lee
- Laboratory of Medicinal Chemistry, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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19
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Cheng J, Wang S, Lin W, Wu N, Wang Y, Chen M, Xie XQ, Feng Z. Computational Systems Pharmacology-Target Mapping for Fentanyl-Laced Cocaine Overdose. ACS Chem Neurosci 2019; 10:3486-3499. [PMID: 31257858 DOI: 10.1021/acschemneuro.9b00109] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The United States of America is fighting against one of its worst-ever drug crises. Over 900 people a week die from opioid- or heroin-related overdoses, while millions more suffer from opioid prescription addiction. Recently, drug overdoses caused by fentanyl-laced cocaine specifically are on the rise. Due to drug synergy and an increase in side effects, polydrug addiction can cause more risk than addiction to a single drug. In the present work, we systematically analyzed the overdose and addiction mechanism of cocaine and fentanyl. First, we applied our established chemogenomics knowledgebase and machine-learning-based methods to map out the potential and known proteins, transporters, and metabolic enzymes and the potential therapeutic target(s) for cocaine and fentanyl. Sequentially, we looked into the detail of (1) the addiction to cocaine and fentanyl by binding to the dopamine transporter and the μ opioid receptor (DAT and μOR, respectively), (2) the potential drug-drug interaction of cocaine and fentanyl via p-glycoprotein (P-gp) efflux, (3) the metabolism of cocaine and fentanyl in CYP3A4, and (4) the physiologically based pharmacokinetic (PBPK) model for two drugs and their drug-drug interaction at the absorption, distribution, metabolism, and excretion (ADME) level. Finally, we looked into the detail of JWH133, an agonist of cannabinoid 2-receptor (CB2) with potential as a therapy for cocaine and fentanyl overdose. All these results provide a better understanding of fentanyl and cocaine polydrug addiction and future drug abuse prevention.
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Affiliation(s)
- Jin Cheng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Pharmacy, Jiangsu Vocational College of Medicine, Yancheng, Jiangsu 224005, China
| | - Siyi Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Weiwei Lin
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Nan Wu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Yuanqiang Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Maozi Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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20
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Khan MT, Malik SI. Structural dynamics behind variants in pyrazinamidase and pyrazinamide resistance. J Biomol Struct Dyn 2019; 38:3003-3017. [PMID: 31357912 DOI: 10.1080/07391102.2019.1650113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Pyrazinamide (PZA) is an important component of first-line anti-tuberculosis (anti-TB) drugs. The anti-TB agent is activated into an active form, pyrazinoic acid (POA), by Mycobacterium tuberculosis (MTB) pncA gene encoding pyrazinamidase (PZase). The major cause of PZA-resistance has been associated with mutations in the pncA gene. We have detected several novel mutations including V131F, Q141P, R154T, A170P, and V180F (GeneBank Accession No. MH461111) in the pncA gene of PZA-resistant isolates during PZA drug susceptibility testing followed by pncA gene sequencing. Here, we investigated molecular mechanism of PZA-resistance by comparing the results of experimental and molecular dynamics. The mutants (MTs) and wild type (WT) PZase structures in apo and complex with PZA were subjected to molecular dynamic simulations (MD) at the 40 ns. Multiple factors, including root mean square deviations (RMSD), binding pocket, total energy, dynamic cross correlation, and root mean square fluctuations (RMSF) of MTs and WT were compared. The MTs attained a high deviation and fluctuation compared to WT. Binding pocket volumes of the MTs, were found, lower than the WT, and the docking scores were high than WT while shape complementarity scores were lower than that of the WT. Residual motion in MTs are seemed to be dominant in anti-correlated motion. Mutations at locations, V131F, Q141P, R154T, A170P, and V180F, might be involved in the structural changes, possibly affecting the catalytic property of PZase to convert PZA into POA. Our study provides useful information that will enhance the understanding for better management of TB. AbbreviationsDSTdrug susceptibility testingΔelecelectrostatic energyLJLowenstein-Jensen mediumMGITmycobacterium growth indicator tubesMTsmutantsMDmolecular dynamic simulationsMTBMycobacterium tuberculosisNALC-NaOHN-acetyl-l-cysteine-sodium hydroxideNIHNational Institutes of HealthNPTamount of substance (N), pressure (P) temperature (T)NVTmoles (N), volume (V) temperature (T)PZasepyrazinamidaseΔpspolar solvation energyPTRLProvincial Tuberculosis Reference LaboratoryRMSDroot mean square deviationsRMSFroot mean square fluctuationsΔSASAsolvent accessible surface area energyTBtuberculosisGTotaltotal binding free energyΔvdWVan der Waals energyWTwild typeCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
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21
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Chen M, Jing Y, Wang L, Feng Z, Xie XQ. DAKB-GPCRs: An Integrated Computational Platform for Drug Abuse Related GPCRs. J Chem Inf Model 2019; 59:1283-1289. [PMID: 30835466 PMCID: PMC6758544 DOI: 10.1021/acs.jcim.8b00623] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Drug abuse (DA) or drug addiction is a complicated brain disorder which is commonly considered as neurobiological impairments caused by both genetic factors and environmental effects. Among DA-related targets, G protein-coupled receptors (GPCRs) play an important role in DA therapy. However, only 52 GPCRs have been published with crystal structures in the recent two decades. In the effort to overcome the limitations of crystal structure and conformational diversity of GPCRs, we built homology models and performed conformational searches by molecular dynamics (MD) simulation. To accelerate and facilitate the drug abuse research, we construct a DA-related GPCR-specific chemogenomics knowledgebase (KB) (DAKB-GPCRs) for its research that can be implemented with our established and novel chemogenomics tools as well as algorithms for data analysis and visualization. Our established TargetHunter and HTDocking tools, as well as our novel tools that include target classification and Spider Plot, are compiled into the platform. Our DAKB-GPCRs provides the following results for a query compound: (1) blood-brain barrier (BBB) plot via our BBB predictor, (2) docking scores via HTDocking, (3) similarity score via TargetHunter, (4) target classification via machine learning methods that utilize both docking scores and similarity scores, and (5) a drug-target interaction network via Spider Plot.
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Affiliation(s)
- Maozi Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, Pennsylvania 15261, United States
- NIH National Center of Excellence for Computational Drug Abuse Research, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, Pittsburgh, Pennsylvania 15261, United States
| | - Yankang Jing
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, Pennsylvania 15261, United States
- NIH National Center of Excellence for Computational Drug Abuse Research, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, Pittsburgh, Pennsylvania 15261, United States
| | - Lirong Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, Pennsylvania 15261, United States
- NIH National Center of Excellence for Computational Drug Abuse Research, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, Pittsburgh, Pennsylvania 15261, United States
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, Pennsylvania 15261, United States
- NIH National Center of Excellence for Computational Drug Abuse Research, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, Pittsburgh, Pennsylvania 15261, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, Pennsylvania 15261, United States
- NIH National Center of Excellence for Computational Drug Abuse Research, Pittsburgh, Pennsylvania 15261, United States
- Drug Discovery Institute, Pittsburgh, Pennsylvania 15261, United States
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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22
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Insight of Captagon Abuse by Chemogenomics Knowledgebase-guided Systems Pharmacology Target Mapping Analyses. Sci Rep 2019; 9:2268. [PMID: 30783122 PMCID: PMC6381188 DOI: 10.1038/s41598-018-35449-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 09/10/2018] [Indexed: 12/26/2022] Open
Abstract
Captagon, known by its genetic name Fenethylline, is an addictive drug that complicates the War on Drugs. Captagon has a strong CNS stimulating effect than its primary metabolite, Amphetamine. However, multi-targets issues associated with the drug and metabolites as well as its underlying mechanisms have not been fully defined. In the present work, we applied our established drug-abuse chemogenomics-knowledgebase systems pharmacology approach to conduct targets/off-targets mapping (SP-Targets) investigation of Captagon and its metabolites for hallucination addiction, and also analyzed the cell signaling pathways for both Amphetamine and Theophylline with data mining of available literature. Of note, Amphetamine, an agonist for trace amine-associated receptor 1 (TAAR1) with enhancing dopamine signaling (increase of irritability, aggression, etc.), is the main cause of Captagon addiction; Theophylline, an antagonist that blocks adenosine receptors (e.g. A2aR) in the brain responsible for restlessness and painlessness, may attenuate the behavioral sensitization caused by Amphetamine. We uncovered that Theophylline's metabolism and elimination could be retarded due to competition and/or blockage of the CYP2D6 enzyme by Amphetamine; We also found that the synergies between these two metabolites cause Captagon's psychoactive effects to act faster and far more potently than those of Amphetamine alone. We carried out further molecular docking modeling and molecular dynamics simulation to explore the molecular interactions between Amphetamine and Theophylline and their important GPCRs targets, including TAAR1 and adenosine receptors. All of the systems pharmacology analyses and results will shed light insight into a better understanding of Captagon addiction and future drug abuse prevention.
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23
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Zheng W, Wen H. Heat activation mechanism of TRPV1: New insights from molecular dynamics simulation. Temperature (Austin) 2019; 6:120-131. [PMID: 31286023 DOI: 10.1080/23328940.2019.1578634] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/30/2018] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
Abstract
As a member of the transient receptor potential (TRP) channels superfamily, the TRPV1 channel undergoes a closed-to-open gating transition in response to various physical and chemical stimuli including heat. Thanks to recent progress in cryo-electron microscopy, high-resolution structures are becoming available for various TRP channels including TRPV1. This has enabled us to study the molecular mechanism of TRPV1 channel gating by using molecular simulation. Here we review recent progress in molecular simulations of TRPV1 channel by us and others, with focus on our molecular dynamics (MD) simulations of TRPV1 at different temperatures. While no consensus has been reached on the heat activation mechanism of TRPV1, the simulations have offered specific predictions and models for future experimental studies to test.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, State University of New York at Buffalo, Buffalo, NY, USA
| | - Han Wen
- Department of Physics, State University of New York at Buffalo, Buffalo, NY, USA
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24
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Abstract
Although significant advances in experimental high throughput screening (HTS) have been made for drug lead identification, in silico virtual screening (VS) is indispensable owing to its unique advantage over experimental HTS, target-focused, cheap, and efficient, albeit its disadvantage of producing false positive hits. For both experimental HTS and VS, the quality of screening libraries is crucial and determines the outcome of those studies. In this paper, we first reviewed the recent progress on screening library construction. We realized the urgent need for compiling high-quality screening libraries in drug discovery. Then we compiled a set of screening libraries from about 20 million druglike ZINC molecules by running fingerprint-based similarity searches against known drug molecules. Lastly, the screening libraries were objectively evaluated using 5847 external actives covering more than 2000 drug targets. The result of the assessment is very encouraging. For example, with the Tanimoto coefficient being set to 0.75, 36% of external actives were retrieved and the enrichment factor was 13. Additionally, drug target family specific screening libraries were also constructed and evaluated. The druglike screening libraries are available for download from https://mulan.pharmacy.pitt.edu .
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Affiliation(s)
- Junmei Wang
- Department of Pharmaceutical Sciences , The University of Pittsburgh , 3501 Terrace Street , Pittsburgh , Pennsylvania 15261 , United States
| | - Yubin Ge
- Department of Pharmaceutical Sciences , The University of Pittsburgh , 3501 Terrace Street , Pittsburgh , Pennsylvania 15261 , United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences , The University of Pittsburgh , 3501 Terrace Street , Pittsburgh , Pennsylvania 15261 , United States
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25
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Thongnum K, Chanthai S. Inhibitory Reactivity of Capsaicin with α-Amylase and α-Glucosidase Related to Antidiabetes using Molecular Docking and Quantum Calculation Methods. ACTA ACUST UNITED AC 2018. [DOI: 10.13005/ojc/340501] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This work aims to investigate the inhibitory activity of capsaicin, which is one of capsaicinoid compounds, on these enzymes using a molecular docking and quantum calculation. Acarbose, a commercial diabetes drug, was also investigated for comparison. The docking results revealed that acarbose yields better inhibition efficiency with binding free energy (ΔGbinding) of about -8.2 to -11.9 kcal/mol, and inhibition constant (Ki) of about 0.0002 to 0.4 µM, whereas capsaicin provided the ΔGbinding of -5.8 to -6.1 kcal/mol and Ki of 23.7 to 45.9 µM. The total binding energy (ΔEbinding) between each inhibitor and amino acids in active site of enzyme obtained from quantum calculation with MP2/6-31G(d,p) level is in agreement with the ΔGbinding, i.e. the ΔEbinding of acarbose was larger negative than that of capsaicin. The amino acids interacting with inhibitor as hydrogen bond mainly contribute to the total binding energy. Nevertheless, it could be concluded that capsaicinoids have high potential to be developed as an alternative drug for diabetes disease.
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Affiliation(s)
- Kultida Thongnum
- Materials Chemistry Research Center, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Saksit Chanthai
- Materials Chemistry Research Center, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
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26
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Wang Y, Lin W, Wu N, He X, Wang J, Feng Z, Xie XQ. An insight into paracetamol and its metabolites using molecular docking and molecular dynamics simulation. J Mol Model 2018; 24:243. [PMID: 30121710 PMCID: PMC6733030 DOI: 10.1007/s00894-018-3790-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/09/2018] [Indexed: 10/28/2022]
Abstract
Paracetamol is a relatively safe analgesia/antipyretic drug without the risks of addiction, dependence, tolerance, and withdrawal when used alone. However, when administrated in an opioid/paracetamol combination product, which often contains a large quantity of paracetamol, it can be potentially dangerous due to the risk of hepatotoxicity. Paracetamol is known to be metabolized into N-(4-hydroxyphenyl)-arachidonamide (AM404) via fatty acid amide hydrolase (FAAH) and into N-acetyl-p-benzoquinone imine (NAPQI) via cytochrome P450 (CYP) enzymes. However, the underlying mechanism of paracetamol is still unclear. In addition, paracetamol has the potential to interact with other drugs that are also involved with CYP family enzymes (inducer/inhibitor/substrate), an example being illicit drugs. In our present work, we looked into the relationship between paracetamol and its metabolites (AM404 and NAPQI) using molecular docking and molecular dynamics (MD) simulations. We first carried out a series of molecular docking studies between paracetamol/AM404/NAQPI and their reported targets, including CYP 2E1, FAAH, TRPA1, CB1, and TRPV1. Subsequently, we performed MD simulations and energy decomposition for CB1-AM404, TRPV1-AM404, and TRPV1-NAPQI for further investigation of the dynamics interactions. Finally, we summarized and discussed the reported drug-drug interactions between paracetamol and central nervous system drugs, especially illicit drugs. Overall, we are able to provide new insights into the structural and functional roles of paracetamol and its metabolites that can inform the potential prevention and treatment of paracetamol overdose. Graphical abstract Paracetamol and its metabolites.
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Affiliation(s)
- Yuanqiang Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
- Chongqing Key Laboratory of Medicinal Chemistry and Molecular Pharmacology, Chongqing, 400054, China
- Chongqing Key Laboratory of Target Based Drug Screening and Effect Evaluation, Chongqing, 400054, China
| | - Weiwei Lin
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Nan Wu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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27
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Oka H, Yonezawa K, Kamikawa A, Ikegai K, Asai N, Shirakami S, Miyamoto S, Watanabe T, Kiso T, Takemoto Y, Tamura S, Kuramochi T. Design, synthesis, and biological evaluation of novel biphenyl-4-carboxamide derivatives as orally available TRPV1 antagonists. Bioorg Med Chem 2018; 26:3716-3726. [DOI: 10.1016/j.bmc.2018.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/01/2018] [Accepted: 06/01/2018] [Indexed: 01/03/2023]
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28
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The efficacy and safety of cilostazol as an alternative to aspirin in Chinese patients with aspirin intolerance after coronary stent implantation: a combined clinical study and computational system pharmacology analysis. Acta Pharmacol Sin 2018; 39:205-212. [PMID: 28933424 DOI: 10.1038/aps.2017.85] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/19/2017] [Indexed: 12/18/2022] Open
Abstract
Dual antiplatelet therapy (DAT) with aspirin and clopidogrel is the standard regimen to achieve rapid platelet inhibition and prevent thrombotic events. Currently, little information is available regarding alternative antiplatelet therapy in patients with an allergy or intolerance to aspirin. Although cilostazol is already a common alternative to aspirin in clinical practice in China, its efficacy and safety remain to be determined. We retrospectively analyzed 613 Chinese patients who had undergone primary percutaneous coronary intervention (PCI). Among them, 405 patients received standard DAT (aspirin plus clopidogrel) and 205 patients were identified with intolerance to aspirin and received alternative DAT (cilostazol plus clopidogrel). There were no significant differences between the two groups in their baseline clinical characteristics. The main outcomes of the study included major adverse cardiac events (MACEs) and bleeding events during 12 months of follow-up. The MACEs endpoint was reached in 10 of 205 patients treated with cilostazol (4.9%) and in 34 of 408 patients treated with aspirin (8.3%). No statistically significant difference was observed in MACEs between the two groups. However, patients in the cilostazol group had less restenosis than did patients in the aspirin group (1.5% vs 4.9%, P=0.035). The occurrence of bleeding events tended to be lower in the cilostazol group (0.49% vs 2.7%, P=0.063). These clinical observations were further analyzed using network system pharmacology analysis, and the outcomes were consistent with clinical observations and preclinical data reports. We conclude that in Chinese patients with aspirin intolerance undergoing coronary stent implantation, the combination of clopidogrel with cilostazol may be an efficacious and safe alternative to the standard DAT regimen.
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29
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Allosteric Modulation of Intact γ-Secretase Structural Dynamics. Biophys J 2018; 113:2634-2649. [PMID: 29262358 DOI: 10.1016/j.bpj.2017.10.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/26/2017] [Accepted: 10/10/2017] [Indexed: 12/20/2022] Open
Abstract
As a protease complex involved in the cleavage of amyloid precursor proteins that lead to the formation of amyloid β fibrils implicated in Alzheimer's disease, γ-secretase is an important target for developing therapeutics against Alzheimer's disease. γ-secretase is composed of four subunits: nicastrin (NCT) in the extracellular (EC) domain, presenilin-1 (PS1), anterior pharynx defective 1, and presenilin enhancer 2 in the transmembrane (TM) domain. NCT and PS1 play important roles in binding amyloid β precursor proteins and modulating PS1 catalytic activity. Yet, the molecular mechanisms of coupling between substrate/modulator binding and catalytic activity remain to be elucidated. Recent determination of intact human γ-secretase cryo-electron microscopy structure has opened the way for a detailed investigation of the structural dynamics of this complex. Our analysis, based on a membrane-coupled anisotropic network model, reveals two types of NCT motions, bending and twisting, with respect to PS1. These underlie the fluctuations between the "open" and "closed" states of the lid-like NCT with respect to a hydrophilic loop 1 (HL1) on PS1, thus allowing or blocking access of the substrate peptide (EC portion) to HL1 and to the neighboring helix TM2. In addition to this alternating access mechanism, fluctuations in the volume of the PS1 central cavity facilitate the exposure of the catalytic site for substrate cleavage. Druggability simulations show that γ-secretase presents several hot spots for either orthosteric or allosteric inhibition of catalytic activity, consistent with experimental data. In particular, a hinge region at the interface between the EC and TM domains, near the interlobe groove of NCT, emerges as an allo-targeting site that would impact the coupling between HL1/TM2 and the catalytic pocket, opening, to our knowledge, new avenues for structure-based design of novel allosteric modulators of γ-secretase protease activity.
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30
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Hughes TET, Lodowski DT, Huynh KW, Yazici A, Del Rosario J, Kapoor A, Basak S, Samanta A, Han X, Chakrapani S, Zhou ZH, Filizola M, Rohacs T, Han S, Moiseenkova-Bell VY. Structural basis of TRPV5 channel inhibition by econazole revealed by cryo-EM. Nat Struct Mol Biol 2018; 25:53-60. [PMID: 29323279 PMCID: PMC5951624 DOI: 10.1038/s41594-017-0009-1] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 11/13/2017] [Indexed: 12/18/2022]
Abstract
The transient receptor potential vanilloid 5 (TRPV5) channel is a member of the transient receptor potential (TRP) channel family, which is highly selective for Ca2+, that is present primarily at the apical membrane of distal tubule epithelial cells in the kidney and plays a key role in Ca2+ reabsorption. Here we present the structure of the full-length rabbit TRPV5 channel as determined using cryo-EM in complex with its inhibitor econazole. This structure reveals that econazole resides in a hydrophobic pocket analogous to that occupied by phosphatidylinositides and vanilloids in TRPV1, thus suggesting conserved mechanisms for ligand recognition and lipid binding among TRPV channels. The econazole-bound TRPV5 structure adopts a closed conformation with a distinct lower gate that occludes Ca2+ permeation through the channel. Structural comparisons between TRPV5 and other TRPV channels, complemented with molecular dynamics (MD) simulations of the econazole-bound TRPV5 structure, allowed us to gain mechanistic insight into TRPV5 channel inhibition by small molecules.
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Affiliation(s)
- Taylor E T Hughes
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - David T Lodowski
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Kevin W Huynh
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Aysenur Yazici
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - John Del Rosario
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Abhijeet Kapoor
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sandip Basak
- Department of Physiology and Biophysics School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Amrita Samanta
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Physiology and Biophysics School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Xu Han
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sudha Chakrapani
- Department of Physiology and Biophysics School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Z Hong Zhou
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tibor Rohacs
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Seungil Han
- Pfizer Research and Development, Groton, CT, USA
| | - Vera Y Moiseenkova-Bell
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Physiology and Biophysics School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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31
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Martínez-Archundia M, Colín-Astudillo B, Moreno-Vargas LM, Ramírez-Galicia G, Garduño-Juárez R, Deeb O, Contreras-Romo MC, Quintanar-Stephano A, Abarca-Rojano E, Correa-Basurto J. Ligand recognition properties of the vasopressin V2 receptor studied under QSAR and molecular modeling strategies. Chem Biol Drug Des 2017; 90:840-853. [DOI: 10.1111/cbdd.13005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 04/06/2017] [Accepted: 04/08/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Marlet Martínez-Archundia
- Laboratorio de Modelado Molecular y Diseño de Fármacos; Escuela Superior de Medicina-Instituto Politécnico Nacional; México City Mexico
| | - Brenda Colín-Astudillo
- Laboratorio de Modelado Molecular y Diseño de Fármacos; Escuela Superior de Medicina-Instituto Politécnico Nacional; México City Mexico
| | - Liliana M. Moreno-Vargas
- Unidad de Investigación en Enfermedades Oncológicas; Hospital Infantil de México; Mexico City México
| | | | - Ramón Garduño-Juárez
- Instituto de Ciencias Físicas; Universidad Nacional Autónoma de México; Cuernavaca Morelos Mexico
| | - Omar Deeb
- Faculty of Pharmacy; Al-Quds University; Jerusalem Palestine
| | - Martha Citlalli Contreras-Romo
- Departamento de Fisiología y Farmacología; Centro de Ciencias Básicas; Universidad Autónoma de Aguascalientes; Aguascalientes Mexico
| | - Andres Quintanar-Stephano
- Departamento de Fisiología y Farmacología; Centro de Ciencias Básicas; Universidad Autónoma de Aguascalientes; Aguascalientes Mexico
| | - Edgar Abarca-Rojano
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina; Instituto Politécnico Nacional; Mexico DF Mexico
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular y Diseño de Fármacos; Escuela Superior de Medicina-Instituto Politécnico Nacional; México City Mexico
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32
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Pearce LV, Ann J, Jung A, Thorat SA, Herold BKA, Habtemichael AD, Blumberg PM, Lee J. Novel Radiolabeled Vanilloid with Enhanced Specificity for Human Transient Receptor Potential Vanilloid 1 (TRPV1). J Med Chem 2017; 60:8246-8252. [PMID: 28892388 DOI: 10.1021/acs.jmedchem.7b00859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Transient receptor potential vanilloid 1 (TRPV1) has emerged as a promising therapeutic target. While radiolabeled resiniferatoxin (RTX) has provided a powerful tool for characterization of vanilloid binding to TRPV1, TRPV1 shows 20-fold weaker binding to the human TRPV1 than to the rodent TRPV1. We now describe a tritium radiolabeled synthetic vanilloid antagonist, 1-((2-(4-(methyl-[3H])piperidin-1-yl-4-[3H])-6-(trifluoromethyl)pyridin-3-yl)methyl)-3-(3-oxo-3,4-dihydro-2H-benzo[b][1,4]oxazin-8-yl)urea ([3H]MPOU), that embodies improved absolute affinity for human TRPV1 and improved synthetic accessibility.
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Affiliation(s)
- Larry V Pearce
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, Maryland 20892-4255, United States
| | - Jihyae Ann
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul 08826, Republic of Korea
| | - Aeran Jung
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul 08826, Republic of Korea
| | - Shivaji A Thorat
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul 08826, Republic of Korea
| | - Brienna K A Herold
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, Maryland 20892-4255, United States
| | - Amelework D Habtemichael
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, Maryland 20892-4255, United States
| | - Peter M Blumberg
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, Maryland 20892-4255, United States
| | - Jeewoo Lee
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul 08826, Republic of Korea
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33
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Lee S, Kim C, Ann J, Thorat SA, Kim E, Park J, Choi S, Blumberg PM, Frank-Foltyn R, Bahrenberg G, Stockhausen H, Christoph T, Lee J. Pyrazole C-region analogues of 2-(3-fluoro-4-methylsulfonylaminophenyl)propanamides as potent TRPV1 antagonists. Bioorg Med Chem Lett 2017; 27:4383-4388. [PMID: 28838698 DOI: 10.1016/j.bmcl.2017.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/08/2017] [Accepted: 08/10/2017] [Indexed: 10/19/2022]
Abstract
A series of 1-substituted 3-(t-butyl/trifluoromethyl)pyrazole C-region analogues of 2-(3-fluoro-4-methylsulfonamidophenyl)propanamides were investigated for hTRPV1 antagonism. The structure activity relationship indicated that the 3-chlorophenyl group at the 1-position of pyrazole was the optimized hydrophobic group for antagonistic potency and the activity was stereospecific to the S-configuration, providing exceptionally potent antagonists 13S and 16S with Ki(CAP)=0.1nM. Particularly significant, 13S exhibited antagonism selective for capsaicin and NADA and not for low pH or elevated temperature. Both compounds also proved to be very potent antagonists for rTRPV1, blocking in vivo the hypothermic action of capsaicin, consistent with their in vitro mechanism. The docking study of compounds 13S and 16S in our hTRPV1 homology model indicated that the binding modes differed somewhat, with that of 13S more closely resembling that of GRT12360.
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Affiliation(s)
- Sunho Lee
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Changhoon Kim
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jihyae Ann
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Shivaji A Thorat
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eunhye Kim
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jongmi Park
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sun Choi
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Peter M Blumberg
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | | | | | | | - Jeewoo Lee
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
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Chen S, Feng Z, Wang Y, Ma S, Hu Z, Yang P, Chai Y, Xie X. Discovery of Novel Ligands for TNF-α and TNF Receptor-1 through Structure-Based Virtual Screening and Biological Assay. J Chem Inf Model 2017; 57:1101-1111. [PMID: 28422491 PMCID: PMC6732210 DOI: 10.1021/acs.jcim.6b00672] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Tumor necrosis factor α (TNF-α) is overexpressed in various diseases, and it has been a validated therapeutic target for autoimmune diseases. All therapeutics currently used to target TNF-α are biomacromolecules, and limited numbers of TNF-α chemical inhibitors have been reported, which makes the identification of small-molecule alternatives an urgent need. Recent studies have mainly focused on identifying small molecules that directly bind to TNF-α or TNF receptor-1 (TNFR1), inhibit the interaction between TNF-α and TNFR1, and/or regulate related signaling pathways. In this study, we combined in silico methods with biophysical and cell-based assays to identify novel antagonists that bind to TNF-α or TNFR1. Pharmacophore model filtering and molecular docking were applied to identify potential TNF-α antagonists. In regard to TNFR1, we constructed a three-dimensional model of the TNF-α-TNFR1 complex and carried out molecular dynamics simulations to sample the conformations. The residues in TNF-α that have been reported to play important roles in the TNF-α-TNFR1 complex were removed to form a pocket for further virtual screening of TNFR1-binding ligands. We obtained 20 virtual hits and tested them using surface plasmon resonance-based assays, which resulted in one ligand that binds to TNFR1 and four ligands with different scaffolds that bind to TNF-α. T1 and R1, the two most active compounds with Kd values of 11 and 16 μM for TNF-α and TNFR1, respectively, showed activities similar to those of known antagonists. Further cell-based assays also demonstrated that T1 and R1 have similar activities compared to the known TNF-α antagonist C87. Our work has not only produced several TNF-α and TNFR1 antagonists with novel scaffolds for further structural optimization but also showcases the power of our in silico methods for TNF-α- and TNFR1-based drug discovery.
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Affiliation(s)
- Si Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yun Wang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Shifan Ma
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ziheng Hu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Peng Yang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yifeng Chai
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Xiangqun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Lee S, Kang DW, Ryu H, Kim C, Ann J, Lee H, Kim E, Hong S, Choi S, Blumberg PM, Frank-Foltyn R, Bahrenberg G, Stockhausen H, Christoph T, Lee J. t-Butyl pyridine and phenyl C-region analogues of 2-(3-fluoro-4-methylsulfonylaminophenyl)propanamides as potent TRPV1 antagonists. Bioorg Med Chem 2017; 25:2451-2462. [PMID: 28314510 PMCID: PMC6959544 DOI: 10.1016/j.bmc.2017.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/02/2017] [Accepted: 03/02/2017] [Indexed: 01/01/2023]
Abstract
A series of 2-substituted 6-t-butylpyridine and 4-t-butylphenyl C-region analogues of 2-(3-fluoro-4-methylsulfonamidophenyl)propanamides were investigated for hTRPV1 antagonism. The analysis of structure activity relationships indicated that the pyridine derivatives generally exhibited a little better antagonism than did the corresponding phenyl surrogates for most of the series. Among the compounds, compound 7 showed excellent antagonism toward capsaicin activation with Ki=0.1nM and compound 60S demonstrated a strong antiallodynic effect with 83% MPE at 10mg/kg in the neuropathic pain model. The docking study of 7S in our hTRPV1 homology model indicated that the interactions between the A/B-regions of 7S with Tyr511 and the interactions between the t-butyl and ethyl groups in the C-region of 7S with the two hydrophobic binding pockets of hTRPV1 contributed to the high potency.
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Affiliation(s)
- Sunho Lee
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong Wook Kang
- Department of Pharmaceutical Science and Technology, College of Health and Medical Science, Catholic University of Deagu, Gyeongsan-si, Gyeongsangbuk-do 38430, Republic of Korea
| | - HyungChul Ryu
- J2H Biotech, Ansan-si, Gyeonggi-do 15426, Republic of Korea
| | - Changhoon Kim
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jihyae Ann
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hobin Lee
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eunhye Kim
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sunhye Hong
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sun Choi
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Peter M Blumberg
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | | | | | | | - Jeewoo Lee
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
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Kristam R, Rao SN, D’Cruz AS, Mahadevan V, Viswanadhan VN. TRPV1 antagonism by piperazinyl-aryl compounds: A Topomer-CoMFA study and its use in virtual screening for identification of novel antagonists. J Mol Graph Model 2017. [DOI: 10.1016/j.jmgm.2017.01.010 pmid: 28092830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Kristam R, Rao SN, D'Cruz AS, Mahadevan V, Viswanadhan VN. TRPV1 antagonism by piperazinyl-aryl compounds: A Topomer-CoMFA study and its use in virtual screening for identification of novel antagonists. J Mol Graph Model 2017; 72:112-128. [PMID: 28092830 DOI: 10.1016/j.jmgm.2017.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 12/08/2016] [Accepted: 01/06/2017] [Indexed: 11/25/2022]
Abstract
Transient Receptor Potential Vanilloid, member 1 (TRPV1), is a non-selective cation channel belonging to the transient receptor potential (TRP) family of ion channels. It occurs in the peripheral and central nervous system, activated by a variety of exogenous and endogenous stimuli, thus playing a key role in transmission of pain. This has been a target for chronic pain since more than a decade and a number of antagonists that progressed into clinical trials have failed due to the unexpected side effect of core body temperature rise, thus halting progress in this field. Of late, there has been an upsurge in research on this target, with the rat TRPV1 structure being determined, many new antagonists discovered that are temperature-neutral and many new therapeutic avenues being discovered for TRPV1, including diseases of respiratory and digestive systems, skin and bladder. Towards identifying diverse compounds to decipher the role of this target in various indications, here we report a 3D-QSAR model built using the new topomer-CoMFA methodology on a series of piperazinyl-aryl TRPV1 antagonists and the use of this model, along with a pharmacophore model and the shape of one of the potent compounds of this series, to virtually screen a subset of the ZINC database to find novel and diverse hits. These can serve as starting points to develop modality-selective antagonists for chronic pain and to elucidate the critical role of TRPV1 in the various new therapeutic areas.
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Affiliation(s)
- Rajendra Kristam
- Department of Computational Chemistry, Jubilant Biosys Ltd. #96, Industrial Suburb, 2nd Stage, Yeshwanthpur, Bangalore 560 064, India; School of Chemical & Biotechnology, Shanmugha Arts, Science, Technology, and Research Academy (SASTRA University), Thanjavur, Tamil Nadu 613 402, India.
| | - Shashidhar N Rao
- Tripos International, A Certara Company, St. Louis, MO 63101, USA
| | - Anne Sudha D'Cruz
- Department of Computational Chemistry, Jubilant Biosys Ltd. #96, Industrial Suburb, 2nd Stage, Yeshwanthpur, Bangalore 560 064, India
| | - Vijayalakshmi Mahadevan
- School of Chemical & Biotechnology, Shanmugha Arts, Science, Technology, and Research Academy (SASTRA University), Thanjavur, Tamil Nadu 613 402, India
| | - Vellarkad N Viswanadhan
- Department of Computational Chemistry, Jubilant Biosys Ltd. #96, Industrial Suburb, 2nd Stage, Yeshwanthpur, Bangalore 560 064, India
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Zhang H, Ma S, Feng Z, Wang D, Li C, Cao Y, Chen X, Liu A, Zhu Z, Zhang J, Zhang G, Chai Y, Wang L, Xie XQ. Cardiovascular Disease Chemogenomics Knowledgebase-guided Target Identification and Drug Synergy Mechanism Study of an Herbal Formula. Sci Rep 2016; 6:33963. [PMID: 27678063 PMCID: PMC5039409 DOI: 10.1038/srep33963] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 08/25/2016] [Indexed: 12/14/2022] Open
Abstract
Combination therapy is a popular treatment for various diseases in the clinic. Among the successful cases, Traditional Chinese Medicinal (TCM) formulae can achieve synergistic effects in therapeutics and antagonistic effects in toxicity. However, characterizing the underlying molecular synergisms for the combination of drugs remains a challenging task due to high experimental expenses and complication of multicomponent herbal medicines. To understand the rationale of combination therapy, we investigated Sini Decoction, a well-known TCM consisting of three herbs, as a model. We applied our established diseases-specific chemogenomics databases and our systems pharmacology approach TargetHunter to explore synergistic mechanisms of Sini Decoction in the treatment of cardiovascular diseases. (1) We constructed a cardiovascular diseases-specific chemogenomics database, including drugs, target proteins, chemicals, and associated pathways. (2) Using our implemented chemoinformatics tools, we mapped out the interaction networks between active ingredients of Sini Decoction and their targets. (3) We also in silico predicted and experimentally confirmed that the side effects can be alleviated by the combination of the components. Overall, our results demonstrated that our cardiovascular disease-specific database was successfully applied for systems pharmacology analysis of a complicated herbal formula in predicting molecular synergetic mechanisms, and led to better understanding of a combinational therapy.
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Affiliation(s)
- Hai Zhang
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Shifan Ma
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Dongyao Wang
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Chengjian Li
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Yan Cao
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Xiaofei Chen
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Aijun Liu
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Zhenyu Zhu
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Junping Zhang
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Guoqing Zhang
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Yifeng Chai
- College of pharmacy, Second Military Medical University; Department of Pharmacy, Third Affiliated Hospital of Second Military Medical University, Shanghai 200433, China
| | - Lirong Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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39
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Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains. Sci Rep 2016; 6:33112. [PMID: 27612191 PMCID: PMC5017144 DOI: 10.1038/srep33112] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 08/22/2016] [Indexed: 12/20/2022] Open
Abstract
Heat-activated transient receptor potential channel TRPV1 is one of the most studied eukaryotic proteins involved in temperature sensation. Upon heating, it exhibits rapid reversible pore gating, which depolarizes neurons and generates action potentials. Underlying molecular details of such effects in the pore region of TRPV1 is of a crucial importance to control temperature responses of the organism. Despite the spatial structure of the channel in both open (O) and closed (C) states is known, microscopic nature of channel gating and mechanism of thermal sensitivity are still poorly understood. In this work, we used unrestrained atomistic molecular dynamics simulations of TRPV1 (without N- and C-terminal cytoplasmic domains) embedded into explicit lipid bilayer in its O- and C-states. We found that the pore domain with its neighboring loops undergoes large temperature-dependent conformational transitions in an asymmetric way, when fragments of only one monomer move with large amplitude, freeing the pore upon heating. Such an asymmetrical gating looks rather biologically relevant because it is faster and more reliable than traditionally proposed “iris-like” symmetric scheme of channel opening. Analysis of structural, dynamic, and hydrophobic organization of the pore domain revealed entropy growth upon TRPV1 gating, which is in line with current concepts of thermal sensitivity.
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40
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TRPV1: A Target for Rational Drug Design. Pharmaceuticals (Basel) 2016; 9:ph9030052. [PMID: 27563913 PMCID: PMC5039505 DOI: 10.3390/ph9030052] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/12/2016] [Accepted: 08/18/2016] [Indexed: 12/18/2022] Open
Abstract
Transient Receptor Potential Vanilloid 1 (TRPV1) is a non-selective, Ca2+ permeable cation channel activated by noxious heat, and chemical ligands, such as capsaicin and resiniferatoxin (RTX). Many compounds have been developed that either activate or inhibit TRPV1, but none of them are in routine clinical practice. This review will discuss the rationale for antagonists and agonists of TRPV1 for pain relief and other conditions, and strategies to develop new, better drugs to target this ion channel, using the newly available high-resolution structures.
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Feng Z, Pearce LV, Zhang Y, Xing C, Herold BKA, Ma S, Hu Z, Turcios NA, Yang P, Tong Q, McCall AK, Blumberg PM, Xie XQ. Multi-Functional Diarylurea Small Molecule Inhibitors of TRPV1 with Therapeutic Potential for Neuroinflammation. AAPS J 2016; 18:898-913. [PMID: 27000851 PMCID: PMC5333490 DOI: 10.1208/s12248-016-9888-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/10/2016] [Indexed: 01/05/2023] Open
Abstract
Transient receptor potential vanilloid type 1 (TRPV1), a heat-sensitive calcium channel protein, contributes to inflammation as well as to acute and persistent pain. Since TRPV1 occupies a central position in pathways of neuronal inflammatory signaling, it represents a highly attractive potential therapeutic target for neuroinflammation. In the present work, we have in silico identified a series of diarylurea analogues for hTRPV1, of which 11 compounds showed activity in the nanomolar to micromolar range as validated by in vitro biological assays. Then, we utilized molecular docking to explore the detailed interactions between TRPV1 and the compounds to understand the contributions of the different substituent groups. Tyr511, Leu518, Leu547, Thr550, Asn551, Arg557, and Leu670 were important for the recognition of the small molecules by TRPV1. A hydrophobic group in R2 or a polar/hydrophilic group in R1 contributed significantly to the activities of the antagonists at TRPV1. In addition, the subtle different binding pose of meta-chloro in place of para-fluoro in the R2 group converted antagonism into partial agonism, as was predicted by our short-term molecular dynamics (MD) simulation and validated by bioassay. Importantly, compound 15, one of our best TRPV1 inhibitors, also showed potential binding affinity (1.39 μM) at cannabinoid receptor 2 (CB2), which is another attractive target for immuno-inflammation diseases. Furthermore, compound 1 and its diarylurea analogues were predicted to target the C-X-C chemokine receptor 2 (CXCR2), although bioassay validation of CXCR2 with these compounds still needs to be performed. This prediction from the modeling is of interest, since CXCR2 is also a potential therapeutic target for chronic inflammatory diseases. Our findings provide novel strategies to develop a small molecule inhibitor to simultaneously target two or more inflammation-related proteins for the treatment of a wide range of inflammatory disorders including neuroinflammation and neurodegenerative diseases with potential synergistic effect.
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Affiliation(s)
- Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Larry V Pearce
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Yu Zhang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Changrui Xing
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Brienna K A Herold
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Shifan Ma
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Ziheng Hu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Noe A Turcios
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Peng Yang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Qin Tong
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Anna K McCall
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland, 20892, USA
| | - Peter M Blumberg
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland, 20892, USA.
- Laboratory of Cancer Biology and Genetics, National Institutes of Health, Building 37, Room 4048B, 37 Convent Drive MSC 4255, Bethesda, Maryland, 20892-4255, USA.
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.
- NIDA National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.
- Departments of Computational Biology and of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, 15261, USA.
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Hu J, Feng Z, Ma S, Zhang Y, Tong Q, Alqarni MH, Gou X, Xie XQ. Difference and Influence of Inactive and Active States of Cannabinoid Receptor Subtype CB2: From Conformation to Drug Discovery. J Chem Inf Model 2016; 56:1152-63. [PMID: 27186994 PMCID: PMC5395206 DOI: 10.1021/acs.jcim.5b00739] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cannabinoid receptor 2 (CB2), a G protein-coupled receptor (GPCR), is a promising target for the treatment of neuropathic pain, osteoporosis, immune system, cancer, and drug abuse. The lack of an experimental three-dimensional CB2 structure has hindered not only the development of studies of conformational differences between the inactive and active CB2 but also the rational discovery of novel functional compounds targeting CB2. In this work, we constructed models of both inactive and active CB2 by homology modeling. Then we conducted two comparative 100 ns molecular dynamics (MD) simulations on the two systems-the active CB2 bound with both the agonist and G protein and the inactive CB2 bound with inverse agonist-to analyze the conformational difference of CB2 proteins and the key residues involved in molecular recognition. Our results showed that the inactive CB2 and the inverse agonist remained stable during the MD simulation. However, during the MD simulations, we observed dynamical details about the breakdown of the "ionic lock" between R131(3.50) and D240(6.30) as well as the outward/inward movements of transmembrane domains of the active CB2 that bind with G proteins and agonist (TM5, TM6, and TM7). All of these results are congruent with the experimental data and recent reports. Moreover, our results indicate that W258(6.48) in TM6 and residues in TM4 (V164(4.56)-L169(4.61)) contribute greatly to the binding of the agonist on the basis of the binding energy decomposition, while residues S180-F183 in extracellular loop 2 (ECL2) may be of importance in recognition of the inverse agonist. Furthermore, pharmacophore modeling and virtual screening were carried out for the inactive and active CB2 models in parallel. Among all 10 hits, two compounds exhibited novel scaffolds and can be used as novel chemical probes for future studies of CB2. Importantly, our studies show that the hits obtained from the inactive CB2 model mainly act as inverse agonist(s) or neutral antagonist(s) at low concentration. Moreover, the hit from the active CB2 model also behaves as a neutral antagonist at low concentration. Our studies provide new insight leading to a better understanding of the structural and conformational differences between two states of CB2 and illuminate the effects of structure on virtual screening and drug design.
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Affiliation(s)
- Jianping Hu
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- College of Chemistry, Leshan Normal University, Leshan, Sichuan 614004, China
- School of Pharmacy and Bioengineering; Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, Sichuan 610106, China
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Shifan Ma
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Yu Zhang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Qin Tong
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Mohammed Hamed Alqarni
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Xiaojun Gou
- School of Pharmacy and Bioengineering; Key Laboratory of Medicinal and Edible Plants Resources Development, Chengdu University, Chengdu, Sichuan 610106, China
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, NIH National Center of Excellence for Computational Drug Abuse Research, Drug Discovery Institute, and Department of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Díaz-Franulic I, Caceres-Molina J, Sepulveda RV, Gonzalez-Nilo F, Latorre R. Structure-Driven Pharmacology of Transient Receptor Potential Channel Vanilloid 1. Mol Pharmacol 2016; 90:300-8. [PMID: 27335334 DOI: 10.1124/mol.116.104430] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 06/16/2016] [Indexed: 01/08/2023] Open
Abstract
The transient receptor potential vanilloid 1 (TRPV1) ion channel is a polymodal receptor that mediates the flux of cations across the membrane in response to several stimuli, including heat, voltage, and ligands. The best known agonist of TRPV1 channels is capsaicin, the pungent component of "hot" chili peppers. In addition, peptides found in the venom of poisonous animals, along with the lipids phosphatidylinositol 4,5-biphosphate, lysophosphatidic acid, and cholesterol, bind to TRPV1 with high affinity to modulate channel gating. Here, we discuss the functional evidence regarding ligand-dependent activation of TRPV1 channels in light of structural data recently obtained by cryoelectron microscopy. This review focuses on the mechanistic insights into ligand binding and allosteric gating of TRPV1 channels and the relevance of accurate polymodal receptor biophysical characterization for drug design in novel pain therapies.
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Affiliation(s)
- Ignacio Díaz-Franulic
- Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile (I.D.-F., R.L., F.G.-N.); Centro de Bioinformática y Biología Integrativa, Universidad Andrés Bello, Santiago, Chile (I.D.-F., J.C.-M., R.V.S., F.G.-N.); and Fraunhofer Chile Research, Santiago, Chile (I.D.-F.)
| | - Javier Caceres-Molina
- Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile (I.D.-F., R.L., F.G.-N.); Centro de Bioinformática y Biología Integrativa, Universidad Andrés Bello, Santiago, Chile (I.D.-F., J.C.-M., R.V.S., F.G.-N.); and Fraunhofer Chile Research, Santiago, Chile (I.D.-F.)
| | - Romina V Sepulveda
- Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile (I.D.-F., R.L., F.G.-N.); Centro de Bioinformática y Biología Integrativa, Universidad Andrés Bello, Santiago, Chile (I.D.-F., J.C.-M., R.V.S., F.G.-N.); and Fraunhofer Chile Research, Santiago, Chile (I.D.-F.)
| | - Fernando Gonzalez-Nilo
- Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile (I.D.-F., R.L., F.G.-N.); Centro de Bioinformática y Biología Integrativa, Universidad Andrés Bello, Santiago, Chile (I.D.-F., J.C.-M., R.V.S., F.G.-N.); and Fraunhofer Chile Research, Santiago, Chile (I.D.-F.)
| | - Ramon Latorre
- Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile (I.D.-F., R.L., F.G.-N.); Centro de Bioinformática y Biología Integrativa, Universidad Andrés Bello, Santiago, Chile (I.D.-F., J.C.-M., R.V.S., F.G.-N.); and Fraunhofer Chile Research, Santiago, Chile (I.D.-F.)
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Metal binding mediated conformational change of XPA protein:a potential cytotoxic mechanism of nickel in the nucleotide excision repair. J Mol Model 2016; 22:156. [PMID: 27307058 DOI: 10.1007/s00894-016-3017-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/26/2016] [Indexed: 12/13/2022]
Abstract
Nucleotide excision repair (NER) is a pivotal life process for repairing DNA nucleotide mismatch caused by chemicals, metal ions, radiation, and other factors. As the initiation step of NER, the xeroderma pigmentosum complementation group A protein (XPA) recognizes damaged DNA molecules, and recruits the replication protein A (RPA), another important player in the NER process. The stability of the Zn(2+)-chelated Zn-finger domain of XPA center core portion (i.e., XPA98-210) is the foundation of its biological functionality, while the displacement of the Zn(2+) by toxic metal ions (such as Ni(2+), a known human carcinogen and allergen) may impair the effectiveness of NER and hence elevate the chance of carcinogenesis. In this study, we first calculated the force field parameters for the bonded model in the metal center of the XPA98-210 system, showing that the calculated results, including charges, bonds, angles etc., are congruent with previously reported results measured by spectrometry experiments and quantum chemistry computation. Then, comparative molecular dynamics simulations using these parameters revealed the changes in the conformation and motion mode of XPA98-210 Zn-finger after the substitution of Zn(2+) by Ni(2+). The results showed that Ni(2+) dramatically disrupted the relative positions of the four Cys residues in the Zn-finger structure, forcing them to collapse from a tetrahedron into an almost planar structure. Finally, we acquired the binding mode of XPA98-210 with its ligands RPA70N and DNA based on molecular docking and structural alignment. We found that XPA98-210's Zn-finger domain primarily binds to a V-shaped cleft in RPA70N, while the cationic band in its C-terminal subdomain participates in the recognition of damaged DNA. In addition, this article sheds light on the multi-component interaction pattern among XPA, DNA, and other NER-related proteins (i.e., RPA70N, RPA70A, RPA70B, RPA70C, RPA32, and RPA14) based on previously reported structural biology information. Thus, we derived a putative cytotoxic mechanism associated with the nickel ion, where the Ni(2+) disrupts the conformation of the XPA Zn-finger, directly weakening its interaction with RPA70N, and thus lowering the effectiveness of the NER process. In sum, this work not only provides a theoretical insight into the multi-protein interactions involved in the NER process and potential cytotoxic mechanism associated with Ni(2+) binding in XPA, but may also facilitate rational anti-cancer drug design based on the NER mechanism.
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Aiello F, Badolato M, Pessina F, Sticozzi C, Maestrini V, Aldinucci C, Luongo L, Guida F, Ligresti A, Artese A, Allarà M, Costa G, Frosini M, Schiano Moriello A, De Petrocellis L, Valacchi G, Alcaro S, Maione S, Di Marzo V, Corelli F, Brizzi A. Design and Synthesis of New Transient Receptor Potential Vanilloid Type-1 (TRPV1) Channel Modulators: Identification, Molecular Modeling Analysis, and Pharmacological Characterization of the N-(4-Hydroxy-3-methoxybenzyl)-4-(thiophen-2-yl)butanamide, a Small Molecule Endowed with Agonist TRPV1 Activity and Protective Effects against Oxidative Stress. ACS Chem Neurosci 2016; 7:737-48. [PMID: 26942555 DOI: 10.1021/acschemneuro.5b00333] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
4-(Thiophen-2-yl)butanoic acid was identified as a cyclic substitute of the unsaturated alkyl chain of the natural ligand, capsaicin. Accordingly, a new class of amides was synthesized in good yield and high purity and their molecular recognition against the target was investigated by means of docking experiments followed by molecular dynamics simulations, in order to rationalize their geometrical and thermodynamic profiles. The pharmacological properties of these new compounds were expressed as activation (EC50) and desensitization (IC50) potencies. Several compounds were found to activate TRPV1 channels, and in particular, derivatives 1 and 10 behaved as TRPV1 agonists endowed with good efficacy as compared to capsaicin. The most promising compound 1 was also evaluated for its protective role against oxidative stress on keratinocytes and differentiated human neuroblastoma cell lines expressing the TRPV1 receptor as well as for its cytotoxicity and analgesic activity in vivo.
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Affiliation(s)
- Francesca Aiello
- Dipartimento
di Farmacia e Scienza della Salute e della Nutrizione, Università della Calabria, Edificio Polifunzionale, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Mariateresa Badolato
- Dipartimento
di Farmacia e Scienza della Salute e della Nutrizione, Università della Calabria, Edificio Polifunzionale, 87036 Arcavacata di Rende, Cosenza, Italy
| | | | - Claudia Sticozzi
- Dipartimento
Scienza della Vita e Biotecnologie, Università degli Studi di Ferrara, Via L. Borsari 46, 44121 Ferrara, Italy
| | | | | | - Livio Luongo
- Dipartimento
di Medicina Sperimentale, Sezione di Farmacologia “L. Donatelli”, Seconda Università di Napoli, 80138 Napoli, Italy
| | - Francesca Guida
- Dipartimento
di Medicina Sperimentale, Sezione di Farmacologia “L. Donatelli”, Seconda Università di Napoli, 80138 Napoli, Italy
| | - Alessia Ligresti
- Istituto
di Chimica Biomolecolare, Endocannabinoid Research Group, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Anna Artese
- Dipartimento
di Scienze della Salute, Università degli Studi “Magna Graecia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Marco Allarà
- Istituto
di Chimica Biomolecolare, Endocannabinoid Research Group, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Giosué Costa
- Dipartimento
di Scienze della Salute, Università degli Studi “Magna Graecia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | | | - Aniello Schiano Moriello
- Istituto
di Chimica Biomolecolare, Endocannabinoid Research Group, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Luciano De Petrocellis
- Istituto
di Chimica Biomolecolare, Endocannabinoid Research Group, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Giuseppe Valacchi
- Dipartimento
Scienza della Vita e Biotecnologie, Università degli Studi di Ferrara, Via L. Borsari 46, 44121 Ferrara, Italy
| | - Stefano Alcaro
- Dipartimento
di Scienze della Salute, Università degli Studi “Magna Graecia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Sabatino Maione
- Dipartimento
di Medicina Sperimentale, Sezione di Farmacologia “L. Donatelli”, Seconda Università di Napoli, 80138 Napoli, Italy
| | - Vincenzo Di Marzo
- Istituto
di Chimica Biomolecolare, Endocannabinoid Research Group, Consiglio Nazionale delle Ricerche, Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
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46
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Ann J, Sun W, Zhou X, Jung A, Baek J, Lee S, Kim C, Yoon S, Hong S, Choi S, Turcios NA, Herold BKA, Esch TE, Lewin NE, Abramovitz A, Pearce LV, Blumberg PM, Lee J. Discovery of N-(3-fluoro-4-methylsulfonamidomethylphenyl)urea as a potent TRPV1 antagonistic template. Bioorg Med Chem Lett 2016; 26:3603-7. [PMID: 27317643 DOI: 10.1016/j.bmcl.2016.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/02/2016] [Accepted: 06/06/2016] [Indexed: 12/21/2022]
Abstract
A series of homologous analogues of prototype antagonist 1 and its urea surrogate were investigated as hTRPV1 ligands. Through one-carbon elongation in the respective pharmacophoric regions, N-(3-fluoro-4-methylsulfonamidomethylphenyl)urea was identified as a novel and potent TRPV1 antagonistic template. Its representative compound 27 showed a potency comparable to that of lead compound 1. Docking analysis of compound 27 in our hTRPV1 homology model indicated that its binding mode was similar with that of 1S.
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Affiliation(s)
- Jihyae Ann
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Wei Sun
- Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xing Zhou
- Hainan Institute of Materia Medica, Haikou 570311, China
| | - Aeran Jung
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jisoo Baek
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Sunho Lee
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Changhoon Kim
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Suyoung Yoon
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Sunhye Hong
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Sun Choi
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Noe A Turcios
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Brienna K A Herold
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Timothy E Esch
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nancy E Lewin
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Adelle Abramovitz
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Larry V Pearce
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Peter M Blumberg
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jeewoo Lee
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea.
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47
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Zhang F, Hanson SM, Jara-Oseguera A, Krepkiy D, Bae C, Pearce LV, Blumberg PM, Newstead S, Swartz KJ. Engineering vanilloid-sensitivity into the rat TRPV2 channel. eLife 2016; 5:e16409. [PMID: 27177419 PMCID: PMC4907692 DOI: 10.7554/elife.16409] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 05/12/2016] [Indexed: 01/08/2023] Open
Abstract
The TRPV1 channel is a detector of noxious stimuli, including heat, acidosis, vanilloid compounds and lipids. The gating mechanisms of the related TRPV2 channel are poorly understood because selective high affinity ligands are not available, and the threshold for heat activation is extremely high (>50°C). Cryo-EM structures of TRPV1 and TRPV2 reveal that they adopt similar structures, and identify a putative vanilloid binding pocket near the internal side of TRPV1. Here we use biochemical and electrophysiological approaches to investigate the resiniferatoxin(RTx) binding site in TRPV1 and to explore the functional relationships between TRPV1 and TRPV2. Collectively, our results support the interaction of vanilloids with the proposed RTx binding pocket, and demonstrate an allosteric influence of a tarantula toxin on vanilloid binding. Moreover, we show that sensitivity to RTx can be engineered into TRPV2, demonstrating that the gating and permeation properties of this channel are similar to TRPV1.
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Affiliation(s)
- Feng Zhang
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Sonya M Hanson
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Andres Jara-Oseguera
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Dmitriy Krepkiy
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Chanhyung Bae
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Larry V Pearce
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Peter M Blumberg
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Kenton J Swartz
- Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
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48
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Ann J, Ki Y, Yoon S, Kim MS, Lee JU, Kim C, Lee S, Jung A, Baek J, Hong S, Choi S, Pearce LV, Esch TE, Turcios NA, Lewin NE, Ogunjirin AE, Herold BKA, McCall AK, Blumberg PM, Lee J. 2-Sulfonamidopyridine C-region analogs of 2-(3-fluoro-4-methylsulfonamidophenyl)propanamides as potent TRPV1 antagonists. Bioorg Med Chem 2016; 24:1231-40. [PMID: 26860926 PMCID: PMC6957252 DOI: 10.1016/j.bmc.2016.01.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 01/25/2016] [Accepted: 01/27/2016] [Indexed: 12/30/2022]
Abstract
A series of 2-sulfonamidopyridine C-region derivatives of 2-(3-fluoro-4-methylsulfonamidophenyl)propanamide were investigated as hTRPV1 ligands. Systematic modification on the 2-sulfonamido group provided highly potent TRPV1 antagonists. The N-benzyl phenylsulfonamide derivatives 12 and 23 in particular showed higher affinities than that of lead compound 1. Compound 12 exhibited strong analgesic activity in the formalin pain model. Docking analysis of its chiral S-form 12S in our hTRPV1 homology model indicated that its high affinity might arise from additional hydrophobic interactions not present in lead compound 1S.
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Affiliation(s)
- Jihyae Ann
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Yooran Ki
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Suyoung Yoon
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Myeong Seop Kim
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jung-Un Lee
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Changhoon Kim
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Sunho Lee
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Aeran Jung
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jisoo Baek
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Sunhye Hong
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Sun Choi
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Larry V Pearce
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Timothy E Esch
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Noe A Turcios
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nancy E Lewin
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Adebowale E Ogunjirin
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Brienna K A Herold
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Anna K McCall
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Peter M Blumberg
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jeewoo Lee
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea.
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49
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Chen X, Lu Y, Tan G, Cao Z, Liu W, Wang B, Zhang M, Li Z. Functional and binding characterization of a single chain Fv antibody to abscisic acid and conjugated abscisic acid. FOOD AGR IMMUNOL 2016. [DOI: 10.1080/09540105.2016.1148123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Xiaojiao Chen
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
| | - Yao Lu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guiyu Tan
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
| | - Zhen Cao
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, USA
| | - Wei Liu
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
| | - Baomin Wang
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
| | - Mingcai Zhang
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
| | - Zhaohu Li
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, China
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50
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Jiang W, Li W, Hong Y, Wang S, Fang B. Cloning, Expression, Mutagenesis Library Construction of Glycerol Dehydratase, and Binding Mode Simulation of Its Reactivase with Ligands. Appl Biochem Biotechnol 2015; 178:739-52. [PMID: 26547853 DOI: 10.1007/s12010-015-1906-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/21/2015] [Indexed: 11/26/2022]
Abstract
The production of 1, 3-propanediol (1, 3-PD) and 3-hydroxypropionaldehyde (3-HPA) by enzyme reaction has been a hot field, and glycerol dehydratase (GDHt) is the key and rate-limiting enzyme involved in their biosynthesis. The gldABC gene encoding GDHt was cloned from Klebsiella pneumoniae, and the activity of the corresponding proteins expressed extracellularly and intracellularly was 6.8 and 3.2 U/mg, respectively, about six and three times higher than that of the wild strain. The change of amino acids for the β subunit can adjust the length of the Co-N bond and affect the homolysis rate of the Co-C bond to change GDHt activity. The expression plasmid, pET-32a-gldAC (containing no gldB which encodes the β subunit of GDHt), was constructed to build the mutagenesis library to improve the GDHt activity. The binding models of glycerol dehydratase reactivation factor (GDHtR) with ATP, CTP, or GTP were simulated by semi-flexible docking, respectively, and there was almost no difference between them. This research provided the basis for studying the quantitative structure-activity relationships between GDHtR and its ligands, as well as searching inexpensive ligands to replace ATP. These results and methods are of great use in economical and highly efficient production of 3-HPA and 1, 3-PD by the enzyme method.
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Affiliation(s)
- Wei Jiang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China
| | - Wenjun Li
- Hangzhou DAC Biotech Co., Ltd, Hangzhou, 310000, China
| | - Yan Hong
- Jingdezhen Ceramic Institute of Materials Science and Engineering, Jingde Zhen, 333000, China
| | - Shizhen Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China
| | - Baishan Fang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, 361005, China.
- The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian, 361005, China.
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