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Renart ML, Giudici AM, González-Ros JM, Poveda JA. Steady-state and time-resolved fluorescent methodologies to characterize the conformational landscape of the selectivity filter of K + channels. Methods 2024; 225:89-99. [PMID: 38508347 DOI: 10.1016/j.ymeth.2024.02.010] [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: 10/13/2023] [Revised: 02/02/2024] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
A variety of equilibrium and non-equilibrium methods have been used in a multidisciplinary approach to study the conformational landscape associated with the binding of different cations to the pore of potassium channels. These binding processes, and the conformational changes resulting therefrom, modulate the functional properties of such integral membrane properties, revealing these permeant and blocking cations as true effectors of such integral membrane proteins. KcsA, a prototypic K+ channel from Streptomyces lividans, has been extensively characterized in this regard. Here, we revise several fluorescence-based approaches to monitor cation binding under different experimental conditions in diluted samples, analyzing the advantages and disadvantages of each approach. These studies have contributed to explain the selectivity, conduction, and inactivation properties of K+ channels at the molecular level, together with the allosteric communication between the two gates that control the ion channel flux, and how they are modulated by lipids.
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Affiliation(s)
- María Lourdes Renart
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
| | - Ana Marcela Giudici
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
| | - José M González-Ros
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
| | - José A Poveda
- IDiBE-Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain.
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Uddin MJ, Niloy SI, Aktaruzzaman M, Talukder MEK, Rahman MM, Imon RR, Uddin AFMS, Amin MZ. Neuropharmacological assessment and identification of possible lead compound (apomorphine) from Hygrophila spinosa through in-vivo and in-silico approaches. J Biomol Struct Dyn 2024:1-16. [PMID: 38385482 DOI: 10.1080/07391102.2024.2317974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The aim of this research is to examine possible neurological activity of methanol, ethyl acetate, and aqueous extracts of Hygrophila spinosa and identify possible lead compounds through in silico analysis. In vivo, neuropharmacological activity was evaluated by using four distinct neuropharmacological assessment assays. Previously reported GC-MS data and earlier literature were utilized to identify the phytochemicals present in Hygrophila spinosa. Computational studies notably molecular docking and molecular dynamic simulations were conducted with responsible receptors to assess the stability of the best interacting compound. Pharmacokinetics properties like absorption, distribution, metabolism, excretion, and toxicity were considered to evaluate the drug likeliness properties of the identified compounds. All the in vivo results support the notion that different extracts (methanol, ethyl acetate, and aqueous) of Hygrophila spinosa have significant (*p = 0.05) sedative-hypnotic, anxiolytic, and anti-depressant activity. Among all the extracts, specifically methanol extracts of Hygrophila spinosa (MHS 400 mg/kg.b.w.) showed better sedative, anxiolytic and antidepressant activity than aqueous and ethyl acetate extracts. In silico molecular docking analysis revealed that among 53 compounds 7 compounds showed good binding affinities and one compound, namely apomorphine (CID: 6005), surprisingly showed promising binding affinity to all the receptors . An analysis of molecular dynamics simulations confirmed that apomorphine (CID: 6005) had a high level of stability at the protein binding site. Evidence suggests that Hygrophila spinosa has significant sedative, anxiolytic, and antidepressant activity. In silico analysis revealed that a particular compound (apomorphine) is responsible for this action. Further research is required in order to establish apomorphine as a drug for anxiety, depression, and sleep disorders.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Jashim Uddin
- Department of Pharmacy, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Clinical Pharmacy and Pharmacology. Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
| | | | - Md Aktaruzzaman
- Department of Pharmacy, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Clinical Pharmacy and Pharmacology. Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Enamul Kabir Talukder
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Mashiar Rahman
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Raihan Rahman Imon
- Molecular and Cellular Biology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - A F M Shahab Uddin
- Department of Computer Science and Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Ziaul Amin
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
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Jyoti MA, Shah MS, Uddin MN, Hossain MK, Han A, Geng P, Islam MN, Mamun AA. Anti-oxidant and neuro-modulatory effects of bioactive Byttneria pilosa leaf extract in swiss albino mice using behavioral models. Front Chem 2024; 12:1341308. [PMID: 38389724 PMCID: PMC10881790 DOI: 10.3389/fchem.2024.1341308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/08/2024] [Indexed: 02/24/2024] Open
Abstract
Byttneria pilosa, a flowering plant from the Malvaceae family traditionally used to treat ailments such as boils and scabies, is here investigated for its potential health benefits. The study focused on evaluating its antioxidant and antidiabetic properties in vitro, as well as the in vivo anxiolytic and antidepressant activities of the methanol extract of B. pilosa leaf (MEBP). The study employed various assays to evaluate antioxidant activity, including 2, 2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, reducing power capacity, and quantification of the total phenolic and flavonoid contents of MEBP. Additionally, anxiolytic and antidepressant activities were evaluated through four tests: elevated plus-maze test (EPMT), light-dark box test (LDBT), forced swimming test (FST), and tail suspension test (TST). Antidiabetic effect was determined using α-amylase inhibition assay. Docking analysis was performed using BIOVIA and Schrödinger Maestro (v11.1), and the absorption, distribution, metabolism, and excretion/toxicity (ADME/T) properties of bioactive substances were investigated using a web-based technique. MEBP exhibited moderate antioxidant activity in DPPH radical scavenging and reducing power capacity assays, with a dose-dependent response. The total phenolic and flavonoid contents measured were 70 ± 1.53 mg and 22.33 ± 1.20 mg, respectively. MEBP demonstrated significant effects in α-amylase inhibition comparable to acarbose. In behavioral tests, MEBP dose-dependently altered time spent in open arms/light box and closed arms/dark box, indicating anxiolytic effects. Moreover, MEBP significantly reduced immobility duration in FST and TST, suggesting antidepressant properties. Molecular docking analysis revealed favorable interactions between beta-sitosterol and specific targets, suggesting the potential mediation of anxiolytic and antidiabetic effects. Overall, MEBP exhibits notable anxiolytic and antidepressant properties, along with moderate antioxidant and antidiabetic activities.
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Affiliation(s)
- Mifta Ahmed Jyoti
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Md Shahin Shah
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Mohammad Najim Uddin
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
- Department of Pharmacy, Faculty of Life and Earth Science, Jagannath University, Dhaka,Bangladesh
| | - Mohammed Kamrul Hossain
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Aixia Han
- Central Laboratory of The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui People's Hospital, Lishui, Zhejiang, China
| | - Peiwu Geng
- Central Laboratory of The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui People's Hospital, Lishui, Zhejiang, China
| | - Mohammad Nazmul Islam
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Abdullah Al Mamun
- Central Laboratory of The Sixth Affiliated Hospital of Wenzhou Medical University, Lishui People's Hospital, Lishui, Zhejiang, China
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Fan C, Flood E, Sukomon N, Agarwal S, Allen TW, Nimigean CM. Calcium-gated potassium channel blockade via membrane-facing fenestrations. Nat Chem Biol 2024; 20:52-61. [PMID: 37653172 PMCID: PMC10847966 DOI: 10.1038/s41589-023-01406-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/18/2023] [Indexed: 09/02/2023]
Abstract
Quaternary ammonium blockers were previously shown to bind in the pore to block both open and closed conformations of large-conductance calcium-activated potassium (BK and MthK) channels. Because blocker entry was assumed through the intracellular entryway (bundle crossing), closed-pore access suggested that the gate was not at the bundle crossing. Structures of closed MthK, a Methanobacterium thermoautotrophicum homolog of BK channels, revealed a tightly constricted intracellular gate, leading us to investigate the membrane-facing fenestrations as alternative pathways for blocker access directly from the membrane. Atomistic free energy simulations showed that intracellular blockers indeed access the pore through the fenestrations, and a mutant channel with narrower fenestrations displayed no closed-state TPeA block at concentrations that blocked the wild-type channel. Apo BK channels display similar fenestrations, suggesting that blockers may use them as access paths into closed channels. Thus, membrane fenestrations represent a non-canonical pathway for selective targeting of specific channel conformations, opening novel ways to selectively drug BK channels.
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Affiliation(s)
- Chen Fan
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria, Australia
- Schrödinger, Inc., New York, NY, USA
| | - Nattakan Sukomon
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Shubhangi Agarwal
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Toby W Allen
- School of Science, RMIT University, Melbourne, Victoria, Australia.
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
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Reza AA, Sakib MA, Nasrin MS, Khan J, Khan MF, Hossen MA, Ali MH, Haque MA. Lasia spinosa (L.) thw. attenuates chemically induced behavioral disorders in experimental and computational models. Heliyon 2023; 9:e16754. [PMID: 37313137 PMCID: PMC10258414 DOI: 10.1016/j.heliyon.2023.e16754] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/11/2023] [Accepted: 05/25/2023] [Indexed: 06/15/2023] Open
Abstract
Lasia spinosa (L.) Thw. (L. spinosa) is widely used as a folk remedy for different physical ailments, and its neurological effects have yet to be assessed. Phytochemicals status of L. spinosa was evaluated by GC-MS analysis. Membrane stabilization test, elevated plus maze (EPM) tests and hole board tests (HBT), tail suspension tests (TST) and thiopental sodium-induced sleeping tests (TISTT) were used to assess anti-inflammatory, anxiolytic and anti-depressant activity. Fourteen compounds have been recorded from GC-MS analysis. The LSCTF showed 68.66 ± 2.46% hemolysis protections (p < 0.05) at 500 μg/mL, whereas LSCHF and LSNHF demonstrated efficiency rates of 68.6 ± 1.46% and 52.46 ± 5.28%, respectively. During EPM tests, LSNHF and LSCTF significantly (p < 0.001) increased the time spent in the open arm (59.88 ± 0.65 s and 50.77 ± 0.67 s, respectively) at the dosages of 400 mg/kg. In HBT, samples exhibited dose-dependent anxiolytic activity. LSNHF and LSCTF showed a significant (p < 0.001) hole poking tendency and a high number of head dips (78.66 ± 1.05 and 65.17 ± 0.96, respectively) at the higher dose. In TST, at 400 mg/kg dose demonstrated significantly (p < 0.001) smaller amounts of time immobile, at 81.33 ± 1.67 s and 83.50 ± 1.90 s, respectively, compared to the control group. A consistent finding was also observed in TISTT. The computer-assisted studies on the identified compounds strongly support the aforementioned biological activities, indicating that L. spinosa has potential as a source of medication for treating neuropsychiatric and inflammatory diseases.
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Affiliation(s)
- A.S.M. Ali Reza
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Mahfuz Ahmed Sakib
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Mst. Samima Nasrin
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Jishan Khan
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Mohammad Forhad Khan
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Md. Amjad Hossen
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Md. Hazrat Ali
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
- Department of Pharmacy, Mawlana Bhashani Science and Technology University, Tangail-1902, Bangladesh
| | - Md. Anwarul Haque
- Department of Pharmacy, Faculty of Science, University of Rajshahi, Rajshahi, 6205, Bangladesh
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Rudra S, Omar Faruque M, Tahamina A, Uddin Emon N, Khalil Al Haidar I, Bokhtear Uddin S. Neuropharmacological and antiproliferative activity of Tetrastigma leucostaphyllum (Dennst.) Alston: Evidence from in-vivo, in-vitro and in-silico approaches. Saudi Pharm J 2023; 31:929-941. [PMID: 37234345 PMCID: PMC10205772 DOI: 10.1016/j.jsps.2023.04.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
As the incidence of neurodegeneration and cancer fatalities remains high, researchers are focusing their efforts on discovering and developing effective medications, especially plant-based drugs, against these diseases. Hence, this research aimed to investigate the neuropharmacological potentials of aerial parts of Tetrastigma leucostaphyllum, employing some behavioral models, while the antiproliferative effect was explored against a panel of cancer cell lines (MGC-803, A549, U-251, HeLa and MCF-7) using a colorimetric assay. In addition, active extracts were analyzed by GC-MS technique to identify the active compounds, where some selective compounds were docked with the particular pure proteins to check their binding affinity. Results from neuropharmacological research indicated that the total extract and its fractions may be effective (p = 0.05, 0.01, and 0.001, respectively) at doses of 100, 200, and 400 mg/kg of animal body weight. The greatest antidepressant and anxiolytic effects were found in the n-hexane fraction. The n-haxane fraction also exhibited the highest cytotoxicity against the U-251 cell line (IC5014.3 μg/mL), followed by the A549, MG-803, HeLa, and MCF-7 cell lines, respectively. From the n-hexane fraction, ten chemicals were detected using the GC-MS method. Additionally, the in-silico research revealed interactions between the n-hexane fractions' identified compounds and the antidepressant, anxiolytic, and cytotoxic receptors. The molecules showed binding affinities that ranged from 4.6 kcal/mol to 6.8 kcal/mol, which indicates the likelihood that they would make good drug candidates. This study highlighted the plant's neuropharmacological and cytotoxic properties, however, more research is needed to determine the etymological origin of these effects.
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Affiliation(s)
- Sajib Rudra
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram 4331, Bangladesh
| | - Mohammad Omar Faruque
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram 4331, Bangladesh
| | - Afroza Tahamina
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram 4331, Bangladesh
| | - Nazim Uddin Emon
- Department of Pharmacy, Faculty of Science and Engineering, International Islamic University Chittagong, Chattogram 4318, Bangladesh
| | | | - Shaikh Bokhtear Uddin
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram 4331, Bangladesh
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Tareq AM, Hossain MM, Uddin M, Islam F, Khan Z, Karim MM, Lyzu C, Ağagündüz D, Reza AA, Emran TB, Capasso R. Chemical profiles and pharmacological attributes of Apis cerana indica beehives using combined experimental and computer-aided studies. Heliyon 2023; 9:e15016. [PMID: 37089286 PMCID: PMC10114209 DOI: 10.1016/j.heliyon.2023.e15016] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
The current study sought to determine the anxiolytic, antidepressant, and anti-inflammatory properties of distilled water-soluble extract of beehive (WSE-BH). Gas chromatography-mass spectrometry (GC-MS) studies were used to characterize the chemical compositions obtained from beehives extracted in water and methanol (also fractions). The GC-MS analysis identified 19 compounds in WSE-BH, including high total phenol and flavonoid contents, compared with the methanol extract (21 compounds), ethyl acetate fraction (9 compounds), and CCl4 fraction (27 compounds). The oral administration of WSE-BH (50 and 150 mg/kg) showed significant anxiolytic activities assessed by time spent in (30.80% and 39.47%, respectively) and entry into (47.49% and 55.93%, respectively) the open arms of the elevated plus-maze (EPM). Only the 150 mg/kg dose resulted in a significant effect on the number of head-dipping events in the hole-board test (HBT) (40.2 ± 2.33; p < 0.01) vs. diazepam (64.33 ± 3.16; p < 0.001). Both the 50 and 150 mg/kg doses resulted in significant (p < 0.001) decreases in immobility in the forced swim test (FST) and tail suspensions test (TST), corresponding to the effect of fluoxetine. WSE-BH inhibited histamine-induced paw edema significantly beginning at 60 min, with the 150 mg/kg dose having the highest effect at 180 min. The current findings suggested that WSE-BH had anxiolytic, antidepressant, and anti-inflammatory properties.
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Affiliation(s)
- Abu Montakim Tareq
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
| | - Md Mohotasin Hossain
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
| | - Main Uddin
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
| | - Farhanul Islam
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
| | - Zidan Khan
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
| | - Md Mobarak Karim
- Department of Biomedical Engineering, University of Houston, TX, USA
| | - Chadni Lyzu
- Biomedical and Toxicological Research Institute, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dr. Qudrat-I-Khuda Road, Dhanmondi, Dhaka, 1205, Bangladesh
| | - Duygu Ağagündüz
- Department of Nutrition and Dietetics, Gazi University, Ankara 06450, Turkey
| | - A.S.M. Ali Reza
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
- Corresponding author. Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh.
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
- Corresponding author. Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh.
| | - Raffaele Capasso
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Naples, Italy
- Corresponding author. Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Naples, Italy.
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Schmidpeter PAM, Petroff JT, Khajoueinejad L, Wague A, Frankfater C, Cheng WWL, Nimigean CM, Riegelhaupt PM. Membrane phospholipids control gating of the mechanosensitive potassium leak channel TREK1. Nat Commun 2023; 14:1077. [PMID: 36841877 PMCID: PMC9968290 DOI: 10.1038/s41467-023-36765-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/15/2023] [Indexed: 02/27/2023] Open
Abstract
Tandem pore domain (K2P) potassium channels modulate resting membrane potentials and shape cellular excitability. For the mechanosensitive subfamily of K2Ps, the composition of phospholipids within the bilayer strongly influences channel activity. To examine the molecular details of K2P lipid modulation, we solved cryo-EM structures of the TREK1 K2P channel bound to either the anionic lipid phosphatidic acid (PA) or the zwitterionic lipid phosphatidylethanolamine (PE). At the extracellular face of TREK1, a PA lipid inserts its hydrocarbon tail into a pocket behind the selectivity filter, causing a structural rearrangement that recapitulates mutations and pharmacology known to activate TREK1. At the cytoplasmic face, PA and PE lipids compete to modulate the conformation of the TREK1 TM4 gating helix. Our findings demonstrate two distinct pathways by which anionic lipids enhance TREK1 activity and provide a framework for a model that integrates lipid gating with the effects of other mechanosensitive K2P modulators.
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Affiliation(s)
| | - John T Petroff
- Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Leila Khajoueinejad
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Aboubacar Wague
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
| | - Cheryl Frankfater
- Department of Endocrinology, Metabolism, and Lipid Research, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Wayland W L Cheng
- Department of Anesthesiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA
| | - Paul M Riegelhaupt
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY, USA.
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V. H. P, M. K. J, H. R. R, Shivamurthy VKN, Patil SM, Shirahatti PS, Ramu R. New insights on the phytochemical intervention for the treatment of neuropsychiatric disorders using the leaves of Michelia champaca: an in vivo and in silico approach. PHARMACEUTICAL BIOLOGY 2022; 60:1656-1668. [PMID: 36052952 PMCID: PMC9448401 DOI: 10.1080/13880209.2022.2101669] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
CONTEXT Michelia champaca L. (Magnoliaceae) has been known since ancient times for its rich medicinal properties. OBJECTIVE The ethanol extract of Michelia champaca leaves (EEMC) was evaluated on depression and anxiety using in vivo and in silico studies. MATERIALS AND METHODS Swiss albino mice were divided into control, standard, 100 and 200 mg/kg b.w. EEMC groups and for drug administration using oral gavage. The antidepressant activity was evaluated using forced swim test (FST) and tail suspension test (TST) whereas the anxiolytic activity through elevated plus maze and light and dark tests. The in silico studies included molecular docking against human potassium channel KCSA-FAB and human serotonin transporter, and ADME/T analysis. RESULTS Open arm duration and entries were comparable between 200 mg/kg b.w. group (184.45 ± 1.00 s and 6.25 ± 1.11, respectively) and that of diazepam treated group (180.02 s ± 0.40 and 6.10 ± 0.05, respectively). Time spent in the light cubicle was higher (46.86 ± 0.03%), similar to that of diazepam (44.33 ± 0.64%), suggesting its potent anxiolytic activity. A delayed onset of immobility and lowered immobility time was seen at both the treatment doses (FST: 93.7 ± 1.70 and 89.1 ± 0.40 s; TST: 35.05 ± 2.75 and 38.50 ± 4.10 s) and the standard drug imipramine (FST: 72.7 ± 3.72 and TST: 30.01 ± 2.99 s), indicative of its antidepressant ability. In silico studies predicted doripenem to induce anxiolytic and antidepressant activity by inhibiting human potassium channel KCSA-FAB and human serotonin transporter proteins, respectively. CONCLUSIONS EEMC is a rich source of bioactive compounds with strong antidepressant and anxiolytic properties.
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Affiliation(s)
- Pushpa V. H.
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, India
- CONTACT Pushpa V. H. Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, Karnataka570015, India
| | - Jayanthi M. K.
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, India
| | - Rashmi H. R.
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru, India
| | - Veeresh Kumar N. Shivamurthy
- Department of Neurology, Saint Francis Hospital and Medical Center, Trinity Health Of New England, Hartford, CT, USA
| | - Shashank M. Patil
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, India
| | - Prithvi S. Shirahatti
- Department of Biotechnology, Teresian College, Mysuru, India
- St. Joseph's College for Women, Mysore, Karnataka, India
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, India
- Ramith Ramu Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru, India
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10
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Biochemical and Pharmacological aspects of Ganoderma lucidum: Exponent from the in vivo and computational investigations. Biochem Biophys Rep 2022; 32:101371. [PMID: 36386440 PMCID: PMC9650014 DOI: 10.1016/j.bbrep.2022.101371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
Ganoderma lucidum is known as lingzhi mushroom, which is said to have medicinal properties by the local residents. This research was focused to assess the antidepressant, anxiolytic, and sedative activities of the mentioned mushroom extracts by means of in vivo and in silico approaches. The antidepressant, anxiolytic, and sedative properties of the methanol extracts of G. lucidum (MEGL) were assessed using the forced swim test hole board, open field test, elevated plus maze, hole cross test, and thiopental sodium-induced sleeping time. The extracts revealed significant antidepressant, anxiolytic, and sedative activities in a dose-dependent manner. Rutin and quercetin were found to be the most effective enzyme inhibitors in the molecular docking study. According to the findings of in vivo and molecular docking study, it could be forecast that, the extract could have substantial antidepressant, anxiolytic, and sedative characteristics and deep molecular strategies on this extracts might create a target for the development of novel therapeutics. Further investigations are needed to appraise the molecular mechanisms implicated and isolate the bioactive components. Rutin and quercetin are reported in Ganoderma lucidum mushroom. The mushroom extracts possessed dose-dependent impacts on neural diseases. Elements of the Ganoderma lucidum yielded prominent binding affinity to the neural receptors. The mushroom extract is non-toxic evident from an acute toxicity study.
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Marquis MJ, Sack JT. Mechanism of use-dependent Kv2 channel inhibition by RY785. J Gen Physiol 2022; 154:e202112981. [PMID: 35435946 PMCID: PMC9195051 DOI: 10.1085/jgp.202112981] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 03/01/2022] [Accepted: 03/30/2022] [Indexed: 01/21/2023] Open
Abstract
Understanding the mechanism by which ion channel modulators act is critical for interpretation of their physiological effects and can provide insight into mechanisms of ion channel gating. The small molecule RY785 is a potent and selective inhibitor of Kv2 voltage-gated K+ channels that has a use-dependent onset of inhibition. Here, we investigate the mechanism of RY785 inhibition of rat Kv2.1 (Kcnb1) channels heterologously expressed in CHO-K1 cells. We find that 1 µM RY785 block eliminates Kv2.1 current at all physiologically relevant voltages, inhibiting ≥98% of the Kv2.1 conductance. Both onset of and recovery from RY785 inhibition require voltage sensor activation. Intracellular tetraethylammonium, a classic open-channel blocker, competes with RY785 inhibition. However, channel opening itself does not appear to alter RY785 access. Gating current measurements reveal that RY785 inhibits a component of voltage sensor activation and accelerates voltage sensor deactivation. We propose that voltage sensor activation opens a path into the central cavity of Kv2.1 where RY785 binds and promotes voltage sensor deactivation, trapping itself inside. This gated-access mechanism in conjunction with slow kinetics of unblock supports simple interpretation of RY785 effects: channel activation is required for block by RY785 to equilibrate, after which trapped RY785 will simply decrease the Kv2 conductance density.
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Affiliation(s)
- Matthew James Marquis
- Department of Physiology & Membrane Biology, University of California, Davis, Davis, CA
| | - Jon T. Sack
- Department of Physiology & Membrane Biology, University of California, Davis, Davis, CA
- Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA
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Deciphering the Pharmacological Potentials of Methanol Extract of Sterculia foetida Seeds Using Experimental and Computational Approaches. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:3403086. [PMID: 35502174 PMCID: PMC9056218 DOI: 10.1155/2022/3403086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/18/2022] [Accepted: 04/04/2022] [Indexed: 11/22/2022]
Abstract
The edible herb Sterculia foetida L. has potential nutraceutical and medicinal effects. The present study is performed to assess the possible antidiabetic, neuropharmacological, and antidiarrheal activity of the methanolic extract of S. foetida seeds (MESF) through in vitro, in vivo, and in silico approaches. When compared to standard acarbose, the results of the antidiabetic study provided strong proof that the glucose level in the MESF was gradually decreased by inhibiting the function of α-amylase enzymes. The sedative potential of MESF (200 and 400 mg/kg) was determined by employing open field, hole cross, and thiopental sodium-induced sleeping time tests, which revealed significant reductions in locomotor performance and increased sleep duration following MESF treatment. In addition, mice treated with MESF exhibited superior exploration during elevated plus maze and hole board tests. MESF also showed good antidiarrheal activity in castor oil-induced diarrhea and intestinal motility tests. Previously isolated compounds (captan, 1-azuleneethanol, acetate, and tetraconazole) exhibited good binding affinity in docking studies and drug-likeliness properties in absorption, distribution, metabolism, excretion/toxicity (ADME/T), and toxicological studies. Collectively, these results indicate the bioactivity of S. foetida, which represents a potential candidate in the food and pharmaceutical industries.
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Gamal El-Din TM, Lenaeus MJ. Fenestropathy of Voltage-Gated Sodium Channels. Front Pharmacol 2022; 13:842645. [PMID: 35222049 PMCID: PMC8873592 DOI: 10.3389/fphar.2022.842645] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/25/2022] [Indexed: 11/17/2022] Open
Abstract
Voltage-gated sodium channels (Nav) are responsible for the initiation and propagation of action potentials in excitable cells. From pain to heartbeat, these integral membrane proteins are the ignition stations for every sensation and action in human bodies. They are large (>200 kDa, 24 transmembrane helices) multi-domain proteins that couple changes in membrane voltage to the gating cycle of the sodium-selective pore. Nav mutations lead to a multitude of diseases - including chronic pain, cardiac arrhythmia, muscle illnesses, and seizure disorders - and a wide variety of currently used therapeutics block Nav. Despite this, the mechanisms of action of Nav blocking drugs are only modestly understood at this time and many questions remain to be answered regarding their state- and voltage-dependence, as well as the role of the hydrophobic membrane access pathways, or fenestrations, in drug ingress or egress. Nav fenestrations, which are pathways that connect the plasma membrane to the central cavity in the pore domain, were discovered through functional studies more than 40 years ago and once thought to be simple pathways. A variety of recent genetic, structural, and pharmacological data, however, shows that these fenestrations are actually key functional regions of Nav that modulate drug binding, lipid binding, and influence gating behaviors. We discovered that some of the disease mutations that cause arrhythmias alter amino acid residues that line the fenestrations of Nav1.5. This indicates that fenestrations may play a critical role in channel’s gating, and that individual genetic variation may also influence drug access through the fenestrations for resting/inactivated state block. In this review, we will discuss the channelopathies associated with these fenestrations, which we collectively name “Fenestropathy,” and how changes in the fenestrations associated with the opening of the intracellular gate could modulate the state-dependent ingress and egress of drugs binding in the central cavity of voltage gated sodium channels.
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Affiliation(s)
- Tamer M. Gamal El-Din
- Department of Pharmacology, University of Washington, Seattle, WA, United States
- *Correspondence: Tamer M. Gamal El-Din, ; Michael J. Lenaeus,
| | - Michael J. Lenaeus
- Department of Pharmacology, University of Washington, Seattle, WA, United States
- Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
- *Correspondence: Tamer M. Gamal El-Din, ; Michael J. Lenaeus,
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Explanation of Structure and Function of kv1.3 Potent Blocker From Mesobuthus eupeus Venom Gland: A New Promise in Drug Development. Jundishapur J Nat Pharm Prod 2022. [DOI: 10.5812/jjnpp.120271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Scorpions and other venomous animals are sought with great concern because venom is a source of novel peptides with exciting features. Some toxins of scorpion venom are effectors of potassium channels. Previous studies strongly support the importance of potassium channel toxins for use as pharmacological tools or potential drugs. Objectives: Here, a three-dimensional (3-D) structure and function of a potent acidic blocker of the human voltage-gated potassium ion channel, Kv1.3, previously identified in the scorpion Mesobuthus eupeus venom gland, were interpreted. Methods: The 3-D structure of meuK2-2 was generated using homology modeling. The interaction of meuK2-2 with the Kv1.3 channel was evaluated using a computational protocol employing peptide-protein docking experiments, pose clustering, and 100 ns molecular dynamic simulations to make the 3-D models of the meuK2-2/Kv1.3 complex trustworthy. Results: A CSα/β (cysteine-stabilized α-helical and β-sheet) fold was found for the 3-D structure of meuK2-2. In a different mechanism from what was identified so far, meuK2-2 binds to both turret and pore loop of Kv1.3 through two key residues (Ala28 and Ser11) and H-bonds. The binding of meuK2-2 induces some conformational changes to Kv1.3. Eventually, the side chain of a positively charged amino acid (His9) occupies the channel's pore. All together blocks the ion permeation pathway. Conclusions: MeuK2-2 could block Kv1.3 by a new mechanism. So, it could be a unique target for further investigations to develop a pharmacological tool and potential drug.
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Small molecule modulation of the Drosophila Slo channel elucidated by cryo-EM. Nat Commun 2021; 12:7164. [PMID: 34887422 PMCID: PMC8660915 DOI: 10.1038/s41467-021-27435-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/18/2021] [Indexed: 12/16/2022] Open
Abstract
Slowpoke (Slo) potassium channels display extraordinarily high conductance, are synergistically activated by a positive transmembrane potential and high intracellular Ca2+ concentrations and are important targets for insecticides and antiparasitic drugs. However, it is unknown how these compounds modulate ion translocation and whether there are insect-specific binding pockets. Here, we report structures of Drosophila Slo in the Ca2+-bound and Ca2+-free form and in complex with the fungal neurotoxin verruculogen and the anthelmintic drug emodepside. Whereas the architecture and gating mechanism of Slo channels are conserved, potential insect-specific binding pockets exist. Verruculogen inhibits K+ transport by blocking the Ca2+-induced activation signal and precludes K+ from entering the selectivity filter. Emodepside decreases the conductance by suboptimal K+ coordination and uncouples ion gating from Ca2+ and voltage sensing. Our results expand the mechanistic understanding of Slo regulation and lay the foundation for the rational design of regulators of Slo and other voltage-gated ion channels. Slowpoke (Slo) channels are voltage-gated potassium channels that are activated by high intracellular Ca2+ concentrations, and they are targets for insecticides and antiparasitic drugs. Here, the authors present the cryo-EM structures of the Drosophila melanogaster Slo channel in the Ca2+-bound and Ca2+-free conformations, as well as in complex with the fungal neurotoxin verruculogen and the anthelmintic drug emodepside and discuss the mechanisms by which they affect the activity of Slo.
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Gabriel TS, Hansen UP, Urban M, Drexler N, Winterstein T, Rauh O, Thiel G, Kast SM, Schroeder I. Asymmetric Interplay Between K + and Blocker and Atomistic Parameters From Physiological Experiments Quantify K + Channel Blocker Release. Front Physiol 2021; 12:737834. [PMID: 34777005 PMCID: PMC8586521 DOI: 10.3389/fphys.2021.737834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022] Open
Abstract
Modulating the activity of ion channels by blockers yields information on both the mode of drug action and on the biophysics of ion transport. Here we investigate the interplay between ions in the selectivity filter (SF) of K+ channels and the release kinetics of the blocker tetrapropylammonium in the model channel KcvNTS. A quantitative expression calculates blocker release rate constants directly from voltage-dependent ion occupation probabilities in the SF. The latter are obtained by a kinetic model of single-channel currents recorded in the absence of the blocker. The resulting model contains only two adjustable parameters of ion-blocker interaction and holds for both symmetric and asymmetric ionic conditions. This data-derived model is corroborated by 3D reference interaction site model (3D RISM) calculations on several model systems, which show that the K+ occupation probability is unaffected by the blocker, a direct consequence of the strength of the ion-carbonyl attraction in the SF, independent of the specific protein background. Hence, KcvNTS channel blocker release kinetics can be reduced to a small number of system-specific parameters. The pore-independent asymmetric interplay between K+ and blocker ions potentially allows for generalizing these results to similar potassium channels.
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Affiliation(s)
- Tobias S Gabriel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Ulf-Peter Hansen
- Department of Structural Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Martin Urban
- Physikalische Chemie III, Technische Universita̋t Dortmund, Dortmund, Germany
| | - Nils Drexler
- Institute of Physiology II, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Tobias Winterstein
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Oliver Rauh
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universita̋t Dortmund, Dortmund, Germany
| | - Indra Schroeder
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany.,Institute of Physiology II, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
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Moazzem Hossen S, Akramul Hoque Tanim M, Shahadat Hossain M, Ahmed Sami S, Uddin Emon N. Deciphering the CNS anti-depressant, antioxidant and cytotoxic profiling of methanol and aqueous extracts of Trametes versicolor and molecular interactions of its phenolic compounds. Saudi J Biol Sci 2021; 28:6375-6383. [PMID: 34764755 PMCID: PMC8568997 DOI: 10.1016/j.sjbs.2021.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/12/2021] [Accepted: 07/04/2021] [Indexed: 12/30/2022] Open
Abstract
The present study sought to evaluate the central nervous system (CNS) depressant, antioxidant, and cytotoxicity activity of methanol and aqueous extract of Trametes versicolor (METV and AETV). The CNS activity was assessed by the open field, hole-cross, forced swimming, thiopental sodium-induced sleeping time, hole-board, and rotarod tests in Swiss albino mice. For both extracts, a substantial decrease in locomotion was observed in open field and hole-cross tests. In addition, the molecular docking study has been implemented through Maestro V11.1. The higher dose of METV (400 mg/kg) and the lower dose of AETV (200 mg/kg) exhibited a significant decrease in immobility time in forced swimming test and increased prolongation of sleep in thiopental sodium-induced sleeping time test, respectively. In contrast, a moderate finding was observed for the hole-board and rotarod tests. Additionally, a significant DPPH scavenging assay and a high toxicity effect in brine shrimp lethality assay were observed. Besides, five phenolic compounds, namely baicalin, quercetin, catechin, p-hydroxybenzoic acid, and quinic acid, were used for the molecular docking study, whereas catechin demonstrated the highest binding affinity towards the targets. The findings conclude that the T. versicolor could be an alternative source for CNS anti-depressant and antioxidant activity.
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Affiliation(s)
- S.M. Moazzem Hossen
- Department of Pharmacy, Faculty of Biological Science, University of Chittagong, Chittagong 4331, Bangladesh
| | | | - Mohammad Shahadat Hossain
- Department of Pharmacy, Faculty of Biological Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - Nazim Uddin Emon
- Department of Pharmacy, Faculty of Science and Engineering, International Islamic University Chittagong, Chittagong 4318, Bangladesh
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Evaluation of anxiolytic, sedative, and antioxidant activities of Vitex peduncularis Wall. leaves and investigation of possible lead compounds through molecular docking study. ADVANCES IN TRADITIONAL MEDICINE 2021. [DOI: 10.1007/s13596-020-00461-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Computational Analysis of the Crystal and Cryo-EM Structures of P-Loop Channels with Drugs. Int J Mol Sci 2021; 22:ijms22158143. [PMID: 34360907 PMCID: PMC8348670 DOI: 10.3390/ijms22158143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 12/01/2022] Open
Abstract
The superfamily of P-loop channels includes various potassium channels, voltage-gated sodium and calcium channels, transient receptor potential channels, and ionotropic glutamate receptors. Despite huge structural and functional diversity of the channels, their pore-forming domain has a conserved folding. In the past two decades, scores of atomic-scale structures of P-loop channels with medically important drugs in the inner pore have been published. High structural diversity of these complexes complicates the comparative analysis of these structures. Here we 3D-aligned structures of drug-bound P-loop channels, compared their geometric characteristics, and analyzed the energetics of ligand-channel interactions. In the superimposed structures drugs occupy most of the sterically available space in the inner pore and subunit/repeat interfaces. Cationic groups of some drugs occupy vacant binding sites of permeant ions in the inner pore and selectivity-filter region. Various electroneutral drugs, lipids, and detergent molecules are seen in the interfaces between subunits/repeats. In many structures the drugs strongly interact with lipid and detergent molecules, but physiological relevance of such interactions is unclear. Some eukaryotic sodium and calcium channels have state-dependent or drug-induced π-bulges in the inner helices, which would be difficult to predict. The drug-induced π-bulges may represent a novel mechanism of gating modulation.
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CNS anti-depressant, anxiolytic and analgesic effects of Ganoderma applanatum (mushroom) along with ligand-receptor binding screening provide new insights: Multi-disciplinary approaches. Biochem Biophys Rep 2021; 27:101062. [PMID: 34286108 PMCID: PMC8278240 DOI: 10.1016/j.bbrep.2021.101062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 06/12/2021] [Accepted: 06/24/2021] [Indexed: 11/21/2022] Open
Abstract
This research was designed to evaluate the CNS depressant, anxiolytic, and analgesic action of aqueous and ethanol extract of Ganoderma applanatum, a valuable medicinal fungus used in multiple disorders belongs to Ganodermataceae family. Two extracts of G. applanatum were prepared using distilled water and ethanol as solvents and named AEGA and EEGA. Open field method, rotarod method, tail suspension method, and hole cross method were utilized for the CNS depressant action. In contrast, elevated plus-maze test and hole board method were utilized for the anxiolytic action. For determining the analgesic potential, acetic acid-induced writhing test, hot plate method, and tail immersion test were used. Besides, molecular docking has been implemented by using Discovery studio 2020, UCSF Chimera and PyRx autodock vina. At both doses (200 and 400 mg/kg) of AEGA and EEGA showed significant CNS depressant effect (p < 0.05 to 0.001) against all four tests used for CNS depressant activity. Both doses of AEGA and EEGA exhibited important anxiolytic activity effect (p < 0.05 to 0.001)against the EPM and hole board test. Both doses of AEGA and EEGA also exhibited a potential analgesic effect (p < 0.05 to 0.001) against all three tests used for analgesic action. In addition, in the molecular docking the compounds obtained the scores of −5.2 to −12.8 kcal/mol. Ganoapplanin, sphaeropsidin D and cytosporone C showed the best binding affinity to the selected recptors. It can be concluded that AEGA and EEGA have potential CNS depressant, anxiolytic, and analgesic action, which can be used as a natural antidepressant, anxiolytic, and analgesic source. The mushroom extracts were found to possess dose-dependent potentiality in antidepressant and anxiolytic test on mice model. The mushroom extracts revealed significant inhibition in pain. The mushroom extract is non-toxic evident from acute toxicity study. Ganoderma applanatum can be a prominent source of CNS depressant, anxiety and pain management. Ganoderma applanatum is a bracket fungus with a cosmopolitan distribution.
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Deeper Insights on Cnesmone javanica Blume Leaves Extract: Chemical Profiles, Biological Attributes, Network Pharmacology and Molecular Docking. PLANTS 2021; 10:plants10040728. [PMID: 33917986 PMCID: PMC8068331 DOI: 10.3390/plants10040728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 01/14/2023]
Abstract
This study assessed the anxiolytic and antidepressant activities of a methanol leaves extract of Cnesmone javanica (CV) in Swiss albino mice. The study found a significant increase in the percentage of time spent in the open arms of an elevated plus maze and in the incidence of head dipping in hole-board tests following the administration of 400 mg/kg of CV or 1 mg/kg diazepam. Moreover, a significant (p < 0.001) dose-dependent reduction was observed in the immobility time following CV (200 and 400 mg/kg) and fluoxetine (20 mg/kg) administration for forced swimming and tail suspension tests. Gas chromatography–mass spectroscopy (GC–MS) analysis identified 62 compounds in CV, consisting primarily of phenols, terpenoids, esters, and other organic compounds. A molecular docking study was performed to assess the anxiolytic and antidepressant effects of 45 selected compounds against human serotonin transporter and potassium channels receptors. Network pharmacology was performed to predict the pathways involved in these neuropharmacological effects. Overall, CV demonstrated significant and dose-dependent anxiolytic and antidepressant effects due to the presence of several bioactive phytoconstituents, which should be further explored using more advanced and in-depth mechanistic research.
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Moni JNR, Adnan M, Tareq AM, Kabir MI, Reza AA, Nasrin MS, Chowdhury KH, Sayem SAJ, Rahman MA, Alam AHMK, Alam SB, Sakib MA, Oh KK, Cho DH, Capasso R. Therapeutic Potentials of Syzygium fruticosum Fruit (Seed) Reflected into an Array of Pharmacological Assays and Prospective Receptors-Mediated Pathways. Life (Basel) 2021; 11:life11020155. [PMID: 33671381 PMCID: PMC7921944 DOI: 10.3390/life11020155] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 11/16/2022] Open
Abstract
Syzygium fruticosum (SF), a valuable Bangladeshi fruit, is considered an alternative therapeutic agent. Mainly, seeds are used as nutritional phytotherapy to ease physical and mental status by preventing chronic diseases. Here, we scrutinized the S. fruticosum seed's fundamental importance in traditional medicine by following an integrated approach combining in vivo, in vitro, and in silico studies. The SF was fractionated with different solvents, and the ethyl acetate fraction of SF (EaF-SF) was further studied. Mice treated with EaF-SF (200 and 400 mg/kg) manifested anxiolysis evidenced by higher exploration in elevated plus maze and hole board tests. Similarly, a dose-dependent drop of immobility time in a forced swimming test ensured significant anti-depressant activity. Moreover, higher dose treatment exposed reduced exploratory behaviour resembling decreased movement and prolonged sleeping latency with a quick onset of sleep during the open field and thiopental-induced sleeping tests, respectively. In parallel, EaF-SF significantly (p < 0.001) and dose-dependently suppressed acetic acid and formalin-induced pain in mice. Also, a noteworthy anti-inflammatory activity and a substantial (p < 0.01) clot lysis activity (thrombolytic) was observed. Gas chromatography-mass spectrometry (GC-MS) analysis resulted in 49 bioactive compounds. Among them, 12 bioactive compounds with Lipinski's rule and safety confirmation showed strong binding affinity (molecular docking) against the receptors of each model used. To conclude, the S. fruticosum seed is a prospective source of health-promoting effects that can be an excellent candidate for preventing degenerative diseases.
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Affiliation(s)
- Jannatul Nasma Rupa Moni
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (J.N.R.M.); (A.M.T.); (M.S.N.); (K.H.C.); (S.A.J.S.); (S.B.A.); (M.A.S.)
| | - Md. Adnan
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (M.A.); (K.K.O.)
| | - Abu Montakim Tareq
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (J.N.R.M.); (A.M.T.); (M.S.N.); (K.H.C.); (S.A.J.S.); (S.B.A.); (M.A.S.)
| | - Md. Imtiazul Kabir
- Department of Pharmaceutical Science, South Dakota State University, Bookings, SD 57006, USA;
| | - A.S.M. Ali Reza
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (J.N.R.M.); (A.M.T.); (M.S.N.); (K.H.C.); (S.A.J.S.); (S.B.A.); (M.A.S.)
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh;
- Correspondence: (A.S.M.A.R.); (D.H.C.); (R.C.)
| | - Mst. Samima Nasrin
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (J.N.R.M.); (A.M.T.); (M.S.N.); (K.H.C.); (S.A.J.S.); (S.B.A.); (M.A.S.)
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Kamrul Hasan Chowdhury
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (J.N.R.M.); (A.M.T.); (M.S.N.); (K.H.C.); (S.A.J.S.); (S.B.A.); (M.A.S.)
| | - Syed Al Jawad Sayem
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (J.N.R.M.); (A.M.T.); (M.S.N.); (K.H.C.); (S.A.J.S.); (S.B.A.); (M.A.S.)
| | - Md Atiar Rahman
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh;
| | - AHM Khurshid Alam
- Department of Pharmacy, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Seema Binte Alam
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (J.N.R.M.); (A.M.T.); (M.S.N.); (K.H.C.); (S.A.J.S.); (S.B.A.); (M.A.S.)
| | - Mahfuz Ahmed Sakib
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (J.N.R.M.); (A.M.T.); (M.S.N.); (K.H.C.); (S.A.J.S.); (S.B.A.); (M.A.S.)
| | - Ki Kwang Oh
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (M.A.); (K.K.O.)
| | - Dong Ha Cho
- Department of Bio-Health Convergence, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Korea; (M.A.); (K.K.O.)
- Correspondence: (A.S.M.A.R.); (D.H.C.); (R.C.)
| | - Raffaele Capasso
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
- Correspondence: (A.S.M.A.R.); (D.H.C.); (R.C.)
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Chemical Profiles and Pharmacological Properties with in Silico Studies on Elatostema papillosum Wedd. Molecules 2021; 26:molecules26040809. [PMID: 33557235 PMCID: PMC7913918 DOI: 10.3390/molecules26040809] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
The current study attempted, for the first time, to qualitatively and quantitatively determine the phytochemical components of Elatostema papillosum methanol extract and their biological activities. The present study represents an effort to correlate our previously reported biological activities with a computational study, including molecular docking, and ADME/T (absorption, distribution, metabolism, and excretion/toxicity) analyses, to identify the phytochemicals that are potentially responsible for the antioxidant, antidepressant, anxiolytic, analgesic, and anti-inflammatory activities of this plant. In the gas chromatography-mass spectroscopy analysis, a total of 24 compounds were identified, seven of which were documented as being bioactive based on their binding affinities. These seven were subjected to molecular docking studies that were correlated with the pharmacological outcomes. Additionally, the ADME/T properties of these compounds were evaluated to determine their drug-like properties and toxicity levels. The seven selected, isolated compounds displayed favorable binding affinities to potassium channels, human serotonin receptor, cyclooxygenase-1 (COX-1), COX-2, nuclear factor (NF)-κB, and human peroxiredoxin 5 receptor proteins. Phytol acetate, and terpene compounds identified in E. papillosum displayed strong predictive binding affinities towards the human serotonin receptor. Furthermore, 3-trifluoroacetoxypentadecane showed a significant binding affinity for the KcsA potassium channel. Eicosanal showed the highest predicted binding affinity towards the human peroxiredoxin 5 receptor. All of these findings support the observed in vivo antidepressant and anxiolytic effects and the in vitro antioxidant effects observed for this extract. The identified compounds from E. papillosum showed the lowest binding affinities towards COX-1, COX-2, and NF-κB receptors, which indicated the inconsequential impacts of this extract against the activities of these three proteins. Overall, E. papillosum appears to be bioactive and could represent a potential source for the development of alternative medicines; however, further analytical experiments remain necessary.
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24
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Schmidt M, Schroeder I, Bauer D, Thiel G, Hamacher K. Inferring functional units in ion channel pores via relative entropy. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:37-57. [PMID: 33523249 PMCID: PMC7872957 DOI: 10.1007/s00249-020-01480-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 10/11/2020] [Accepted: 11/09/2020] [Indexed: 11/25/2022]
Abstract
Coarse-grained protein models approximate the first-principle physical potentials. Among those modeling approaches, the relative entropy framework yields promising and physically sound results, in which a mapping from the target protein structure and dynamics to a model is defined and subsequently adjusted by an entropy minimization of the model parameters. Minimization of the relative entropy is equivalent to maximization of the likelihood of reproduction of (configurational ensemble) observations by the model. In this study, we extend the relative entropy minimization procedure beyond parameter fitting by a second optimization level, which identifies the optimal mapping to a (dimension-reduced) topology. We consider anisotropic network models of a diverse set of ion channels and assess our findings by comparison to experimental results.
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Affiliation(s)
- Michael Schmidt
- Department of Physics, TU Darmstadt, Karolinenpl. 5, 64289 Darmstadt, Germany
| | - Indra Schroeder
- Department of Biology, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Daniel Bauer
- Department of Biology, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Gerhard Thiel
- Department of Biology, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Kay Hamacher
- Department of Physics, Department of Biology, Department of Computer Science, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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25
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Emon NU, Alam S, Rudra S, Riya SR, Paul A, Hossen SMM, Kulsum U, Ganguly A. Antidepressant, anxiolytic, antipyretic, and thrombolytic profiling of methanol extract of the aerial part of Piper nigrum: In vivo, in vitro, and in silico approaches. Food Sci Nutr 2021; 9:833-846. [PMID: 33598167 PMCID: PMC7866625 DOI: 10.1002/fsn3.2047] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/12/2020] [Accepted: 11/21/2020] [Indexed: 12/20/2022] Open
Abstract
Piper nigrum L. also called black pepper is popular for its numerous uses. The present research is designed to investigate the pharmacological potential of methanol extract of Piper nigrum (MEPN). The antidepressant investigation was performed by using both in vivo forced swimming test (FST) and tail suspension test (TST) methods while the anxiolytic research by hole-board test (HBT) method. Again, the antipyretic analysis was conducted through yeast-induced pyrexia method, whereas clot lysis activity was employed by the thrombolytic method. Furthermore, in silico studies followed by molecular docking analysis of several secondary metabolites, pass prediction, and ADME/T were evaluated with AutoDock Vina, Discovery Studio 2020, UCSF Chimera software PASS online, and ADME/T online tools. The plant extract demonstrated dose-dependent potentiality in antidepressant, anxiolytic, antipyretic, and thrombolytic activities. Induction of MEPN produced a significant (p < .5, p < .001) increase of mobility in FST and TST, and increased the head dipping and decreased the latency of time (p < .01, p < .001) in HBT. MEPN 400 (mg/kg; b.w.; p.o.) lowered the rectal temperature of yeast-induced pyrexia substantially (p < .001). Besides, MEPN produced promising (p < .001) clot lysis activity. In the computational approach, among all the proteins, a docking score was found ranging from -1.0 to -7.90 kcal/mol. Besides, all the compounds were found safe in ADME/T study. The results of our scientific research validate the suitability of this plant as an alternative source of novel therapeutics.
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Affiliation(s)
- Nazim Uddin Emon
- Department of PharmacyInternational Islamic University ChittagongChittagongBangladesh
| | - Safaet Alam
- Department of PharmacyState University of BangladeshDhakaBangladesh
| | - Sajib Rudra
- Department of BotanyUniversity ChittagongChittagongBangladesh
| | | | - Avi Paul
- Department of PharmacySouthern University BangladeshChittagongBangladesh
| | | | - Ummay Kulsum
- Department of PharmacyInternational Islamic University ChittagongChittagongBangladesh
| | - Amlan Ganguly
- Department of Clinical Pharmacy and PharmacologyUniversity of DhakaDhakaBangladesh
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26
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Cholasseri R, De S. Dual-Site Binding of Quaternary Ammonium Ions as Internal K +-Ion Channel Blockers: Nonclassical (C-H···O) H Bonding vs Dispersive (C-H···H-C) Interaction. J Phys Chem B 2021; 125:86-100. [PMID: 33371683 DOI: 10.1021/acs.jpcb.0c09604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular-level study of the influence of the alkyl chain length of quaternary ammonium ions (QAs) on the blocking action and the mode of binding with the bacterial KcsA K+-ion channel is carried out by molecular dynamics (MD) simulations as well as quantum mechanics/molecular mechanics (QM/MM) methods. The present work unveils distinct modes of binding for different QAs, due to differences in size and hydrophobicity. The QAs bind near the channel gate as well as at the central cavity, leading to a possible dual-site blocking action. Small-sized tetraethylammonium (TEA) and tetrabutylammonium (TBA) ions enter inside the channel cavity in the open state of KcsA but bind strongly in the closed state. TEA binds to the polar hydroxyl group of threonine residues situated at the channel gate via nonclassical H-bonding interaction (C-H···O), while TBA binds to a second binding site, the central cavity, with hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues via alkyl-π and hydrophobic interactions (C-H···H-C). On the contrary, large tetrahexylammonium (THA) and tetraoctylammonium (TOA) ions bind the hydrophobic side-chain methyl and isopropyl of alanine and valine at the channel gate both in the open and closed states, thereby restricting the free movement of large QAs toward the center of the cavity. However, the binding to the hydrophobic benzyl and sec-butyl side chains of phenylalanine and isoleucine residues in the closed state is thermodynamically preferable. Also, the binding energy is found to increase with an increase in the alkyl chain length from ethyl (-16.4 kcal/mol) to octyl (-65.5 kcal/mol), due to an almost linear increase in dispersive interaction.
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Affiliation(s)
- Rinsha Cholasseri
- Theoretical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673 601, India
| | - Susmita De
- Department of Applied Chemistry, Cochin University of Science and Technology, Trikakkara, Kochi, Kerala 682 022, India.,Inter University Centre for Nanomaterials and Devices, Cochin University of Science and Technology, Trikakkara, Kochi, Kerala 682 022, India
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27
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Giudici AM, Díaz-García C, Renart ML, Coutinho A, Prieto M, González-Ros JM, Poveda JA. Tetraoctylammonium, a Long Chain Quaternary Ammonium Blocker, Promotes a Noncollapsed, Resting-Like Inactivated State in KcsA. Int J Mol Sci 2021; 22:ijms22020490. [PMID: 33419017 PMCID: PMC7825302 DOI: 10.3390/ijms22020490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/28/2020] [Accepted: 01/01/2021] [Indexed: 02/06/2023] Open
Abstract
Alkylammonium salts have been used extensively to study the structure and function of potassium channels. Here, we use the hydrophobic tetraoctylammonium (TOA+) to shed light on the structure of the inactivated state of KcsA, a tetrameric prokaryotic potassium channel that serves as a model to its homologous eukaryotic counterparts. By the combined use of a thermal denaturation assay and the analysis of homo-Förster resonance energy transfer in a mutant channel containing a single tryptophan (W67) per subunit, we found that TOA+ binds the channel cavity with high affinity, either with the inner gate open or closed. Moreover, TOA+ bound at the cavity allosterically shifts the equilibrium of the channel's selectivity filter conformation from conductive to an inactivated-like form. The inactivated TOA+-KcsA complex exhibits a loss in the affinity towards permeant K+ at pH 7.0, when the channel is in its closed state, but maintains the two sets of K+ binding sites and the W67-W67 intersubunit distances characteristic of the selectivity filter in the channel resting state. Thus, the TOA+-bound state differs clearly from the collapsed channel state described by X-ray crystallography and claimed to represent the inactivated form of KcsA.
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Affiliation(s)
- Ana Marcela Giudici
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
| | - Clara Díaz-García
- Institute for Bioengineering and Bioscience (IBB), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (A.C.); (M.P.)
| | - Maria Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
| | - Ana Coutinho
- Institute for Bioengineering and Bioscience (IBB), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (A.C.); (M.P.)
- Departamento de Química e Bioquímica, Faculty of Sciences, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Manuel Prieto
- Institute for Bioengineering and Bioscience (IBB), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (A.C.); (M.P.)
| | - José M. González-Ros
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
- Correspondence: (J.M.G.-R.); (J.A.P.); Tel.: +34-966-658-757 (J.M.G.-R.); +34-966-658-466 (J.A.P.)
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Instituto de Biología Molecular y Celular (IBMC), Universidad Miguel Hernández, E-03202 Elche, Spain; (A.M.G.); (M.L.R.)
- Correspondence: (J.M.G.-R.); (J.A.P.); Tel.: +34-966-658-757 (J.M.G.-R.); +34-966-658-466 (J.A.P.)
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28
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Evaluation of pharmacological potentials of the aerial part of Achyranthes aspera L.: in vivo, in vitro and in silico approaches. ADVANCES IN TRADITIONAL MEDICINE 2020. [DOI: 10.1007/s13596-020-00528-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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29
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Unravelling the Biological Activities of the Byttneria pilosa Leaves Using Experimental and Computational Approaches. Molecules 2020; 25:molecules25204737. [PMID: 33076534 PMCID: PMC7587548 DOI: 10.3390/molecules25204737] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/07/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Byttneria pilosa is locally known as Harijora, and used by the native hill-tract people of Bangladesh for the treatment of rheumatalgia, snake bite, syphilis, fractured bones, elephantiasis and an antidote for poisoning. The present study was carried out to determine the possible anti-inflammatory, analgesic, neuropharmacological and anti-diarrhoeal activity of the methanol extract of B. pilosa leaves (MEBPL) through in vitro, in vivo and in silico approaches. In the anti-inflammatory study, evaluated by membrane stabilizing and protein denaturation methods, MEBPL showed a significant and dose dependent inhibition. The analgesic effect of MEBPL tested by inducing acetic acid and formalin revealed significant inhibition of pain in both tests. During the anxiolytic evaluation, the extract exhibited a significant and dose-dependent reduction of anxiety-like behaviour in mice. Similarly, mice treated with MEBPL demonstrated dose-dependent reduction in locomotion effect in the open field test and increased sedative effect in the thiopental sodium induced sleeping test. MEBPL also showed good anti-diarrheal activity in both castor oil induced diarrheal and intestinal motility tests. Besides, a previously isolated compound (beta-sitosterol) exhibited good binding affinity in docking and drug-likeliness properties in ADME/T studies. Overall, B. pilosa is a biologically active plant and could be a potential source of drug leads, which warrants further advanced study.
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Chowdhury MR, Chowdhury KH, Hanif NB, Sayeed MA, Mouah J, Mahmud I, Kamal AM, Chy MNU, Adnan M. An integrated exploration of pharmacological potencies of Bischofia javanica (Blume) leaves through experimental and computational modeling. Heliyon 2020; 6:e04895. [PMID: 32984603 PMCID: PMC7492998 DOI: 10.1016/j.heliyon.2020.e04895] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/28/2020] [Accepted: 09/07/2020] [Indexed: 12/28/2022] Open
Abstract
Bischofia javanica (Blume), an edible wild plant, has both prospective nutraceutical and therapeutic properties. Here, we intended to explore the pharmacological potentials of the methanol extract of B. javanica (MEBJ) through integrated approaches. Phytochemical screening revealed the presence of important phytoconstituents which were found to be safe during cytotoxicity analysis. The sedative potential of MEBJ (200 and 400 mg/kg) was determined by employing open field, hole cross, and thiopental sodium-induced sleeping time tests, where a significant reduction of the locomotor performance and an enhancement in the duration of sleeping have been observed, respectively. In addition, mice treated with MEBJ exhibited superior exploration during both elevated plus maze and hole board tests. In parallel, anti-diabetic potency was investigated via alpha-amylase inhibitory assay, where a dose-response increase in the percentage of inhibition has been marked. A similar response, such as an increased percentage of clot lysis, was observed during the thrombolytic test. Furthermore, molecular docking was performed with the identified compounds, demonstrated strong binding affinities to the target receptors of the experiments as mentioned above. Also, ADME/T and toxicological parameters verified the drug-like properties of the identified compounds. Collectively, these results indicate bioactivity of Bischofia javanica, which can be a potential candidate in the food and pharmaceutical industries.
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Affiliation(s)
- Md. Riad Chowdhury
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Kamrul Hasan Chowdhury
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Nujhat Binte Hanif
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Mohammed Abu Sayeed
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Jannatul Mouah
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Iftekher Mahmud
- Department of Chemistry, Wayne State University, Detroit, Michigan, 48202, United States
| | - A.T.M. Mostafa Kamal
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Md. Nazim Uddin Chy
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Md. Adnan
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
- Department of Bio-Health Technology, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
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31
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Jahan I, Tona MR, Sharmin S, Sayeed MA, Tania FZ, Paul A, Chy MNU, Rakib A, Emran TB, Simal-Gandara J. GC-MS Phytochemical Profiling, Pharmacological Properties, and In Silico Studies of Chukrasia velutina Leaves: A Novel Source for Bioactive Agents. Molecules 2020; 25:molecules25153536. [PMID: 32748850 PMCID: PMC7436235 DOI: 10.3390/molecules25153536] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 11/30/2022] Open
Abstract
Chukrasia velutina is a local medicinal plant commonly known as chikrassy in Bangladesh, India, China, and other South Asian countries. The leaves, bark, and seeds are vastly used as herbal medicine for fever and diarrhea, and its leaves essential oils are used for antimicrobial purposes. In this study, we discuss the neuropsychiatric properties of C. velutina leaves through several animal models, quantitative and qualitative phytochemical analysis, and computational approaches. Neuropsychiatric effects were performed in rodents on the methanolic extract of C. velutina leaves (MECVL). Antidepressant, anxiolytic, and sedative effects experimented through these rodent models were used such as the force swimming test (FST), tail suspension test (TST), hole board test (HBT), elevated plus maze test (EPMT), light/dark box test (LDBT), open field test (OFT), and hole cross test (HCT). In these rodent models, 200 and 400 mg/kg doses were used which exhibited a significant result in the force swimming and tail suspension test (p < 0.001) for the antidepressant effect. In the anxiolytic study, the results were significant in the hole board, elevated plus maze, and light/dark box test (p < 0.001) for doses of 200 and 400 mg/kg. The result was also significant in the open field and hole cross test (p < 0.001) for sedative action in the sake of similar doses. Moreover, qualitative and quantitative studies were also performed through phytochemical screening and GC-MS analysis, and fifty-seven phytochemical compounds were found. These compounds were analyzed for pharmacokinetics properties using the SwissADME tool and from them, thirty-five compounds were considered for the molecular docking analysis. These phytoconstituents were docking against the human serotonin receptor, potassium channel receptor, and crystal structure of human beta-receptor, where eight of the compounds showed a good binding affinity towards the respective receptors considered to the reference standard drugs. After all of these analyses, it can be said that the secondary metabolite of C. velutina leaves (MECVL) could be a good source for inhibiting the neuropsychiatric disorders which were found on animal models as well as in computational studies.
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Affiliation(s)
- Israt Jahan
- Department of Pharmacy, Faculty of Science and Engineering, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh; (I.J.); (M.R.T.); (M.A.S.); (F.Z.T.); (M.N.U.C.)
| | - Marzia Rahman Tona
- Department of Pharmacy, Faculty of Science and Engineering, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh; (I.J.); (M.R.T.); (M.A.S.); (F.Z.T.); (M.N.U.C.)
| | - Sanjida Sharmin
- Department of Pharmacy, Faculty of Science and Engineering, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh; (I.J.); (M.R.T.); (M.A.S.); (F.Z.T.); (M.N.U.C.)
- Correspondence: (S.S.); (T.B.E.); (J.S.-G.); Tel.: +88-01819-942214 (T.B.E.); +34-988-387000 (J.S.G.)
| | - Mohammed Aktar Sayeed
- Department of Pharmacy, Faculty of Science and Engineering, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh; (I.J.); (M.R.T.); (M.A.S.); (F.Z.T.); (M.N.U.C.)
| | - Fatamatuz Zuhura Tania
- Department of Pharmacy, Faculty of Science and Engineering, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh; (I.J.); (M.R.T.); (M.A.S.); (F.Z.T.); (M.N.U.C.)
| | - Arkajyoti Paul
- Drug Discovery, GUSTO A Research Group, Chittagong 4203, Bangladesh;
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Md. Nazim Uddin Chy
- Department of Pharmacy, Faculty of Science and Engineering, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh; (I.J.); (M.R.T.); (M.A.S.); (F.Z.T.); (M.N.U.C.)
- Drug Discovery, GUSTO A Research Group, Chittagong 4203, Bangladesh;
| | - Ahmed Rakib
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Talha Bin Emran
- Drug Discovery, GUSTO A Research Group, Chittagong 4203, Bangladesh;
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
- Correspondence: (S.S.); (T.B.E.); (J.S.-G.); Tel.: +88-01819-942214 (T.B.E.); +34-988-387000 (J.S.G.)
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of 21 Food Science and Technology, University of Vigo–Ourense Campus, E32004 Ourense, Spain
- Correspondence: (S.S.); (T.B.E.); (J.S.-G.); Tel.: +88-01819-942214 (T.B.E.); +34-988-387000 (J.S.G.)
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32
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Tareq AM, Farhad S, Neshar Uddin A, Hoque M, Nasrin MS, Uddin MMR, Hasan M, Sultana A, Munira MS, Lyzu C, Moazzem Hossen S, Ali Reza A, Emran TB. Chemical profiles, pharmacological properties, and in silico studies provide new insights on Cycas pectinata. Heliyon 2020; 6:e04061. [PMID: 32529070 PMCID: PMC7283161 DOI: 10.1016/j.heliyon.2020.e04061] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/05/2020] [Accepted: 04/20/2020] [Indexed: 01/15/2023] Open
Abstract
The current study aimed to qualitatively and quantitatively determine the phytochemical components of Cycas pectinata methanol extract (MECP), along with its antioxidant, anti-inflammatory, thrombolytic, locomotor, anxiolytic, analgesic, and antidiarrheal activities. The in vitro antioxidant activity was evaluated by DPPH scavenging assay and the total phenol and total flavonoid contents, while the anti-inflammatory activity was evaluated by a protein denaturation assay. The in vivo locomotor effects were examined using the open field test and hole-cross test. The anxiolytic effect was examined using the elevated plus maze (EPM) test, hole-board test (HBT), and light-dark test (LDT), while the analgesic activity was investigated using the acetic acid-induced writhing test. The antidiarrheal effect was evaluated by castor oil-induced diarrhea and gastrointestinal motility. Ten bioactive compounds were selected on the basis of their biological activities and further investigated using in silico molecular docking simulation to correlate with the identified pharmacological properties. Additionally, the ADME properties of the compounds were evaluated according to their drug-likeness profile. MECP had a maximum total phenol content of 209.85 ± 3.40 gallic acid equivalents/g extract and a total flavonoid content of 105.17 ± 3.45 quercetin equivalents/g extract, with an IC50 value of 631.44 μg/mL. MECP (62.5-500 μg/mL) elicited 20.96-38.12% decreased protein denaturation compared to diclofenac sodium (65.40-83.50%), while a 35.72% (P < 0.001) clot lysis activity was observed for the 10 mg/mL concentration. MECP induced a dose-dependent reduction in locomotor activity, with a significant anxiolytic effect. In the analgesic test, MECP (200, 400 mg/kg) showed a 45.12% and 58.82% inhibition in analgesia, and the 400 mg/kg dose elicited a 27.5% inhibition in intestinal motility. These findings suggest that MECP might be effective in treating antioxidant, anti-inflammatory, and neuropharmacological defects, but this requires further study.
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Affiliation(s)
- Abu Montakim Tareq
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
- Society for Interdisciplinary Research and Innovation, Chawkbazar, 4203, Chittagong, Bangladesh
| | - Saifuddin Farhad
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
| | - A.B.M. Neshar Uddin
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
| | - Muminul Hoque
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
| | - Mst. Samima Nasrin
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh
| | - Mir Md. Rokib Uddin
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
| | - Mohiminul Hasan
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
| | - Arafat Sultana
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
| | | | - Chadni Lyzu
- Biomedical and Toxicological Research Institute, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dr. Qudrat-I-Khuda Road, Dhanmondi, Dhaka 1205, Bangladesh
| | - S.M. Moazzem Hossen
- Department of Pharmacy, Faculty of Biological Science, University of Chittagong, Chittagong 4331, Bangladesh
| | - A.S.M. Ali Reza
- Department of Pharmacy, International Islamic University Chittagong, Kumira, Chittagong 4318, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
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Adnan M, Chy MNU, Kamal AM, Chowdhury KAA, Rahman MA, Reza ASMA, Moniruzzaman M, Rony SR, Nasrin MS, Azad MOK, Park CH, Lim YS, Cho DH. Intervention in Neuropsychiatric Disorders by Suppressing Inflammatory and Oxidative Stress Signal and Exploration of In Silico Studies for Potential Lead Compounds from Holigarna caustica (Dennst.) Oken leaves. Biomolecules 2020; 10:E561. [PMID: 32268590 PMCID: PMC7226598 DOI: 10.3390/biom10040561] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/28/2020] [Accepted: 03/30/2020] [Indexed: 12/17/2022] Open
Abstract
Holigarna caustica (Dennst.), a popular plant used in folk medicine in Bangladesh, is often used by the local folk practitioner to treat a variety of chronic diseases. The present research is an attempt to find out an innovative therapeutic prospect for the management of neuropsychiatric disorders. The methanol extract of H. caustica leaves (MEHC) were utilized on various behavioral tests for assessing anxiolytic, anti-depressant, and anti-inflammatory activities. The antioxidant potentials and quantitative phytochemicals were evaluated through spectrophotometric methods. Results revealed that treatment of MEHC (200 and 400 mg/kg) significantly reduced anxiety like behaviors in mice, particularly, 400 mg/kg efficiently improved % of entries and time spent (p < 0.05) in the open arms in elevated plus maze test, whereas, superior head dipping tendency (p < 0.05) was observed in hole-board test. In contrast, mice treated with 200 mg/kg revealed better anxiolytic effect in both open field and hole-cross tests. During antidepressant evaluation, mice administrated with MEHC exhibited active behaviors (swimming and struggling) in forced swimming and tail suspension tests. In parallel, MEHC manifested a noteworthy (p < 0.001) suppression of inflammatory response induced by histamine. The MEHC also showed strong antioxidant activities in 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) (IC50: 57.64 μg/mL) scavenging, H2O2 (IC50: 51.60 μg/mL) scavenging, and ferric reducing power assay. The levels of total phenol, flavonoid, flavonol, condensed tannin, and antioxidant were estimated as higher in MEHC. Moreover, 11 compounds were documented as bioactive, displayed good binding affinities to potassium channel receptor, human serotonin receptor, cyclooxygenase (COX-1 and 2), and xanthine oxidoreductase enzyme targets in molecular docking experiments. Furthermore, ADME/T and Prediction of Activity Spectra for Substances (PASS) analyses exposed their drug-likeness, nontoxic upon consumption, and likely pharmacological actions. Overall, the H. caustica is potentially bioactive as evident by in vivo, in vitro, and computational analysis. Our findings support the folkloric value of this plant, which may provide a potential source towards developing drug leads.
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Affiliation(s)
- Md. Adnan
- Department of Bio-Health Technology, Kangwon National University, Chuncheon 24341, Korea; (M.A.); (M.O.K.A.); (C.H.P.)
| | - Md. Nazim Uddin Chy
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.N.U.C.); (K.A.A.C.); (A.S.M.A.R.); (M.S.N.)
- Drug Discovery, GUSTO A Research Group, Chittagong 4000, Bangladesh
| | - A.T.M. Mostafa Kamal
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.N.U.C.); (K.A.A.C.); (A.S.M.A.R.); (M.S.N.)
| | - Kazi Asfak Ahmed Chowdhury
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.N.U.C.); (K.A.A.C.); (A.S.M.A.R.); (M.S.N.)
| | - Md. Atiar Rahman
- Department of Biochemistry & Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh;
| | - A. S. M. Ali Reza
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.N.U.C.); (K.A.A.C.); (A.S.M.A.R.); (M.S.N.)
| | - Md. Moniruzzaman
- Designated Reference Institute for Chemical Measurement (DRiCM), Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka 1205, Bangladesh;
| | - Satyajit Roy Rony
- BCSIR Laboratories, Chittagong, Bangladesh Council of Scientific & Industrial Research (BCSIR), Chittagong 4220, Bangladesh;
| | - Mst. Samima Nasrin
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.N.U.C.); (K.A.A.C.); (A.S.M.A.R.); (M.S.N.)
| | - Md Obyedul Kalam Azad
- Department of Bio-Health Technology, Kangwon National University, Chuncheon 24341, Korea; (M.A.); (M.O.K.A.); (C.H.P.)
| | - Cheol Ho Park
- Department of Bio-Health Technology, Kangwon National University, Chuncheon 24341, Korea; (M.A.); (M.O.K.A.); (C.H.P.)
| | - Young Seok Lim
- Department of Bio-Health Technology, Kangwon National University, Chuncheon 24341, Korea; (M.A.); (M.O.K.A.); (C.H.P.)
| | - Dong Ha Cho
- Department of Bio-Health Technology, Kangwon National University, Chuncheon 24341, Korea; (M.A.); (M.O.K.A.); (C.H.P.)
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Adnan M, Chy MNU, Kamal AM, Azad MOK, Chowdhury KAA, Kabir MSH, Gupta SD, Chowdhury MAR, Lim YS, Cho DH. Comparative Study of Piper sylvaticum Roxb. Leaves and Stems for Anxiolytic and Antioxidant Properties Through in vivo, in vitro, and in silico Approaches. Biomedicines 2020; 8:E68. [PMID: 32218219 PMCID: PMC7235905 DOI: 10.3390/biomedicines8040068] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 11/18/2022] Open
Abstract
Piper sylvaticum Roxb. is traditionally used by the indigenous people of tropical and subtropical countries like Bangladesh, India, and China for relieving the common cold or a variety of chronic diseases, such as asthma, chronic coughing, piles, rheumatic pain, headaches, wounds, tuberculosis, indigestion, and dyspepsia. This study tested anxiolytic and antioxidant activities by in vivo, in vitro, and in silico experiments for the metabolites extracted (methanol) from the leaves and stems of P. sylvaticum (MEPSL and MEPSS). During the anxiolytic evaluation analyzed by elevated plus maze and hole board tests, MEPSL and MEPSS (200 and 400 mg/kg, body weight) exhibited a significant and dose-dependent reduction of anxiety-like behavior in mice. Similarly, mice treated with MEPSL and MEPSS demonstrated dose-dependent increases in locomotion and CNS simulative effects in open field test. In addition, both extracts (MEPSL and MEPSS) also showed moderate antioxidant activities in DPPH scavenging and ferric reducing power assays compared to the standard, ascorbic acid. In parallel, previously isolated bioactive compounds from this plant were documented and subjected to a molecular docking study to correlate them with the pharmacological outcomes. The selected four major phytocompounds displayed favorable binding affinities to potassium channel and xanthine oxidoreductase enzyme targets in molecular docking experiments. Overall, P. sylvaticum is bioactive, as is evident through experimental and computational analysis. Further experiments are necessary to evaluate purified novel compounds for the clinical evaluation.
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Affiliation(s)
- Md. Adnan
- Department of Bio-Health Technology, Kangwon National University, Chuncheon 24341, Korea; (M.A.); (M.O.K.A.)
| | - Md. Nazim Uddin Chy
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.N.U.C.); (K.A.A.C.); (M.S.H.K.)
- Drug Discovery, GUSTO A Research Group, Chittagong 4000, Bangladesh; (S.D.G.); (M.A.R.C.)
| | - A.T.M. Mostafa Kamal
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.N.U.C.); (K.A.A.C.); (M.S.H.K.)
| | - Md Obyedul Kalam Azad
- Department of Bio-Health Technology, Kangwon National University, Chuncheon 24341, Korea; (M.A.); (M.O.K.A.)
| | - Kazi Asfak Ahmed Chowdhury
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.N.U.C.); (K.A.A.C.); (M.S.H.K.)
| | - Mohammad Shah Hafez Kabir
- Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh; (M.N.U.C.); (K.A.A.C.); (M.S.H.K.)
- Drug Discovery, GUSTO A Research Group, Chittagong 4000, Bangladesh; (S.D.G.); (M.A.R.C.)
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Shaibal Das Gupta
- Drug Discovery, GUSTO A Research Group, Chittagong 4000, Bangladesh; (S.D.G.); (M.A.R.C.)
- Department of Pharmacy, University of Science and Technology Chittagong, Chittagong 4202, Bangladesh
| | - Md. Ashiqur Rahman Chowdhury
- Drug Discovery, GUSTO A Research Group, Chittagong 4000, Bangladesh; (S.D.G.); (M.A.R.C.)
- Department of Chemistry, University of Chittagong, Chittagong 4331, Bangladesh
| | - Young Seok Lim
- Department of Bio-Health Technology, Kangwon National University, Chuncheon 24341, Korea; (M.A.); (M.O.K.A.)
| | - Dong Ha Cho
- Department of Bio-Health Technology, Kangwon National University, Chuncheon 24341, Korea; (M.A.); (M.O.K.A.)
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35
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Unveiling Pharmacological Responses and Potential Targets Insights of Identified Bioactive Constituents of Cuscuta reflexa Roxb. Leaves through In Vivo and In Silico Approaches. Pharmaceuticals (Basel) 2020; 13:ph13030050. [PMID: 32245131 PMCID: PMC7151675 DOI: 10.3390/ph13030050] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 01/02/2023] Open
Abstract
Cuscuta reflexa Roxb. is traditionally used by the indigenous communities of Bangladesh to treat different diseases, such as pain, edema, tumor, jaundice, and skin infections. This study tested neuro-pharmacological, anti-nociceptive, and antidiarrheal activities by in vivo and in silico experiments for the metabolites extracted (methanol) from the leaves of Cuscuta reflexa (MECR). During the anxiolytic evaluation analyzed by elevated plus maze and hole board tests, MECR (200 and 400 mg/kg) exhibited a significant dose-dependent reduction of anxiety-like behavior in mice. Similarly, mice treated with MECR demonstrated a dose-dependent decrease in the time of immobility in both forced swimming and tail suspension tests. In addition, anti-nociceptive activity was assessed by the chemical-induced (acetic acid and formalin) pain models. In both cases, 400 mg/kg was found to be most effective and significantly (p < 0.001) inhibited acetic acid stimulated writhing and formalin-induced licking (pain response) in mice. Furthermore, antidiarrheal efficacy determined by the castor-oil induced diarrheal model manifested an evident inhibition of diarrheal stool frequency. In parallel, previously isolated bioactive compounds were documented based on the biological activities and subjected to in silico studies to correlate with the current pharmacological outcomes. The selected isolated compounds (15) displayed favorable binding affinities to potassium channels, human serotonin receptor, COX-1, COX-2, M3 muscarinic acetylcholine receptor, and 5-HT3 receptor proteins. Additionally, the ADME/T and toxicological properties were justified to unveil their drug-like properties and toxicity level. Overall, Cuscuta reflexa is bioactive and could be a potential source for the development of alternative medicine.
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Teixeira-Duarte CM, Fonseca F, Morais-Cabral JH. Activation of a nucleotide-dependent RCK domain requires binding of a cation cofactor to a conserved site. eLife 2019; 8:50661. [PMID: 31868587 PMCID: PMC6957272 DOI: 10.7554/elife.50661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/22/2019] [Indexed: 12/24/2022] Open
Abstract
RCK domains regulate the activity of K+ channels and transporters in eukaryotic and prokaryotic organisms by responding to ions or nucleotides. The mechanisms of RCK activation by Ca2+ in the eukaryotic BK and bacterial MthK K+ channels are well understood. However, the molecular details of activation in nucleotide-dependent RCK domains are not clear. Through a functional and structural analysis of the mechanism of ATP activation in KtrA, a RCK domain from the B. subtilis KtrAB cation channel, we have found that activation by nucleotide requires binding of cations to an intra-dimer interface site in the RCK dimer. In particular, divalent cations are coordinated by the γ-phosphates of bound-ATP, tethering the two subunits and stabilizing the active state conformation. Strikingly, the binding site residues are highly conserved in many different nucleotide-dependent RCK domains, indicating that divalent cations are a general cofactor in the regulatory mechanism of many nucleotide-dependent RCK domains.
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Affiliation(s)
- Celso M Teixeira-Duarte
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal.,Programa Doutoral em Biologia Molecular e Celular (MCbiology), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Fátima Fonseca
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - João H Morais-Cabral
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
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37
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Ghilini F, Pissinis DE, Miñán A, Schilardi PL, Diaz C. How Functionalized Surfaces Can Inhibit Bacterial Adhesion and Viability. ACS Biomater Sci Eng 2019; 5:4920-4936. [DOI: 10.1021/acsbiomaterials.9b00849] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Fiorela Ghilini
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, UNLP − CONICET, CC16 Suc 4 (1900), La Plata, Buenos Aires, Argentina
| | - Diego E. Pissinis
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, UNLP − CONICET, CC16 Suc 4 (1900), La Plata, Buenos Aires, Argentina
| | - Alejandro Miñán
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, UNLP − CONICET, CC16 Suc 4 (1900), La Plata, Buenos Aires, Argentina
| | - Patricia L. Schilardi
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, UNLP − CONICET, CC16 Suc 4 (1900), La Plata, Buenos Aires, Argentina
| | - Carolina Diaz
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, UNLP − CONICET, CC16 Suc 4 (1900), La Plata, Buenos Aires, Argentina
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38
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Schewe M, Sun H, Mert Ü, Mackenzie A, Pike ACW, Schulz F, Constantin C, Vowinkel KS, Conrad LJ, Kiper AK, Gonzalez W, Musinszki M, Tegtmeier M, Pryde DC, Belabed H, Nazare M, de Groot BL, Decher N, Fakler B, Carpenter EP, Tucker SJ, Baukrowitz T. A pharmacological master key mechanism that unlocks the selectivity filter gate in K + channels. Science 2019; 363:875-880. [PMID: 30792303 DOI: 10.1126/science.aav0569] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/28/2019] [Indexed: 12/13/2022]
Abstract
Potassium (K+) channels have been evolutionarily tuned for activation by diverse biological stimuli, and pharmacological activation is thought to target these specific gating mechanisms. Here we report a class of negatively charged activators (NCAs) that bypass the specific mechanisms but act as master keys to open K+ channels gated at their selectivity filter (SF), including many two-pore domain K+ (K2P) channels, voltage-gated hERG (human ether-à-go-go-related gene) channels and calcium (Ca2+)-activated big-conductance potassium (BK)-type channels. Functional analysis, x-ray crystallography, and molecular dynamics simulations revealed that the NCAs bind to similar sites below the SF, increase pore and SF K+ occupancy, and open the filter gate. These results uncover an unrecognized polypharmacology among K+ channel activators and highlight a filter gating machinery that is conserved across different families of K+ channels with implications for rational drug design.
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Affiliation(s)
- Marcus Schewe
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany.
| | - Han Sun
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Structural Biology, 13125 Berlin, Germany
| | - Ümit Mert
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Alexandra Mackenzie
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK.,OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK.,Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Ashley C W Pike
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Friederike Schulz
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Cristina Constantin
- Institute of Physiology II, Albert-Ludwigs University of Freiburg, 79104 Freiburg, Germany.,Centers for Biological Signaling Studies CIBSS and BIOSS, 79104 Freiburg, Germany
| | - Kirsty S Vowinkel
- Institute of Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, 35037 Marburg, Germany
| | - Linus J Conrad
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK.,Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Aytug K Kiper
- Institute of Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, 35037 Marburg, Germany
| | - Wendy Gonzalez
- Centro de Bioinformatica y Simulacion Molecular, Universidad de Talca, 3465548 Talca, Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, 3465548 Talca, Chile
| | - Marianne Musinszki
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Marie Tegtmeier
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - David C Pryde
- Pfizer Worldwide Medicinal Chemistry, Neuroscience and Pain Research Unit, Portway Building, Granta Park, Great Abington, Cambridgeshire CB21 6GS, UK
| | - Hassane Belabed
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Medicinal Chemistry, 13125 Berlin, Germany
| | - Marc Nazare
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Medicinal Chemistry, 13125 Berlin, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Niels Decher
- Institute of Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, 35037 Marburg, Germany
| | - Bernd Fakler
- Institute of Physiology II, Albert-Ludwigs University of Freiburg, 79104 Freiburg, Germany.,Centers for Biological Signaling Studies CIBSS and BIOSS, 79104 Freiburg, Germany
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK.,OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK
| | - Stephen J Tucker
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK.,Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Thomas Baukrowitz
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany.
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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40
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Gross A. A flexible filter maintains a tight grip. Nat Chem Biol 2019; 15:319-320. [PMID: 30833777 DOI: 10.1038/s41589-019-0248-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Adrian Gross
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA.
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41
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Potassium channel selectivity filter dynamics revealed by single-molecule FRET. Nat Chem Biol 2019; 15:377-383. [PMID: 30833778 PMCID: PMC6430689 DOI: 10.1038/s41589-019-0240-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 01/25/2019] [Indexed: 11/09/2022]
Abstract
Potassium (K) channels exhibit exquisite selectivity for conduction of K+ ions over other cations, particularly Na+. High-resolution structures reveal an archetypal selectivity filter (SF) conformation in which dehydrated K+ ions, but not Na+ ions, are perfectly coordinated. Using single-molecule FRET (smFRET), we show that the SF-forming loop (SF-loop) in KirBac1.1 transitions between constrained and dilated conformations as a function of ion concentration. The constrained conformation, essential for selective K+ permeability, is stabilized by K+ but not Na+ ions. Mutations that render channels nonselective result in dilated and dynamically unstable conformations, independent of the permeant ion. Further, while wild-type KirBac1.1 channels are K+ selective in physiological conditions, Na+ permeates in the absence of K+. Moreover, whereas K+ gradients preferentially support 86Rb+ fluxes, Na+ gradients preferentially support 22Na+ fluxes. This suggests differential ion selectivity in constrained versus dilated states, potentially providing a structural basis for this anomalous mole fraction effect.
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42
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Bonhenry D, Schober R, Schmidt T, Waldherr L, Ettrich RH, Schindl R. Mechanistic insights into the Orai channel by molecular dynamics simulations. Semin Cell Dev Biol 2019; 94:50-58. [PMID: 30639326 DOI: 10.1016/j.semcdb.2019.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/12/2018] [Accepted: 01/05/2019] [Indexed: 10/27/2022]
Abstract
Highly Ca2+ selective channels trigger a large variety of cellular signaling processes in both excitable and non-excitable cells. Among these channels, the Orai channel is unique in its activation mechanism and its structure. It mediates Ca2+ influx into the cytosol with an extremely small unitary conductance over longer time-scales, ranging from minutes up to several hours. Its activation is regulated by the Ca2+ content of the endoplasmic reticulum (ER). Depletion of luminal [Ca2+]ER is sensed by the STIM1 single transmembrane protein that directly binds and gates the Orai1 channel. Orai mediated Ca2+ influx increases cytosolic Ca2+ from 100 nM up to low micromolar range close to the pore and thereby forms Ca2+ microdomains. Hence, these features of the Orai channel can trigger long-term signaling processes without affecting the overall Ca2+ content of a single living cell. Here we focus on the architecture and dynamic conformational changes within the Orai channel. This review summarizes current achievements of molecular dynamics simulations in combination with live cell recordings to address gating and permeation of the Orai channel with molecular precision.
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Affiliation(s)
- Daniel Bonhenry
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Nové Hrady CZ-373 33, Czech Republic.
| | - Romana Schober
- Institute for Biophysics, Johannes Kepler University Linz, A-4040 Linz, Austria
| | - Tony Schmidt
- Gottfried Schatz Research Center, Medical University of Graz, A-8010 Graz, Austria
| | - Linda Waldherr
- Gottfried Schatz Research Center, Medical University of Graz, A-8010 Graz, Austria
| | - Rüdiger H Ettrich
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Nové Hrady CZ-373 33, Czech Republic; College of Biomedical Sciences, Larkin University, Miami, FL 33169, United States
| | - Rainer Schindl
- Gottfried Schatz Research Center, Medical University of Graz, A-8010 Graz, Austria.
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Wu M, White HV, Boehm BA, Meriney CJ, Kerrigan K, Frasso M, Liang M, Gotway EM, Wilcox MR, Johnson JW, Wipf P, Meriney SD. New Cav2 calcium channel gating modifiers with agonist activity and therapeutic potential to treat neuromuscular disease. Neuropharmacology 2017; 131:176-189. [PMID: 29246857 DOI: 10.1016/j.neuropharm.2017.12.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 11/28/2017] [Accepted: 12/10/2017] [Indexed: 12/13/2022]
Abstract
Voltage-gated calcium channels (VGCCs) are critical regulators of many cellular functions, including the activity-dependent release of chemical neurotransmitter from nerve terminals. At nerve terminals, the Cav2 family of VGCCs are closely positioned with neurotransmitter-containing synaptic vesicles. The relationship between calcium ions and transmitter release is such that even subtle changes in calcium flux through VGCCs have a strong influence on the magnitude of transmitter released. Therefore, modulators of the calcium influx at nerve terminals have the potential to strongly affect transmitter release at synapses. We have previously developed novel Cav2-selective VGCC gating modifiers (notably GV-58) that slow the deactivation of VGCC current, increasing total calcium ion flux. Here, we describe ten new gating modifiers based on the GV-58 structure that extend our understanding of the structure-activity relationship for this class of molecules and extend the range of modulation of channel activities. In particular, we show that one of these new compounds (MF-06) was more efficacious than GV-58, another (KK-75) acts more quickly on VGCCs than GV-58, and a third (KK-20) has a mix of increased speed and efficacy. A subset of these new VGCC agonist gating modifiers can increase transmitter release during action potentials at neuromuscular synapses, and as such, show potential as therapeutics for diseases with a presynaptic deficit that results in neuromuscular weakness. Further, several of these new compounds can be useful tool compounds for the study of VGCC gating and function.
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Affiliation(s)
- Man Wu
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Hayley V White
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Blake A Boehm
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Christopher J Meriney
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Kaylan Kerrigan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Michael Frasso
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Mary Liang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Erika M Gotway
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Madeleine R Wilcox
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Jon W Johnson
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Stephen D Meriney
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, United States.
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Unambiguous observation of blocked states reveals altered, blocker-induced, cardiac ryanodine receptor gating. Sci Rep 2016; 6:34452. [PMID: 27703263 PMCID: PMC5050499 DOI: 10.1038/srep34452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/12/2016] [Indexed: 11/08/2022] Open
Abstract
The flow of ions through membrane channels is precisely regulated by gates. The architecture and function of these elements have been studied extensively, shedding light on the mechanisms underlying gating. Recent investigations have focused on ion occupancy of the channel’s selectivity filter and its ability to alter gating, with most studies involving prokaryotic K+ channels. Some studies used large quaternary ammonium blocker molecules to examine the effects of altered ionic flux on gating. However, the absence of blocking events that are visibly distinct from closing events in K+ channels makes unambiguous interpretation of data from single channel recordings difficult. In this study, the large K+ conductance of the RyR2 channel permits direct observation of blocking events as distinct subconductance states and for the first time demonstrates the differential effects of blocker molecules on channel gating. This experimental platform provides valuable insights into mechanisms of blocker-induced modulation of ion channel gating.
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Jorgensen C, Darré L, Oakes V, Torella R, Pryde D, Domene C. Lateral Fenestrations in K(+)-Channels Explored Using Molecular Dynamics Simulations. Mol Pharm 2016; 13:2263-73. [PMID: 27173896 DOI: 10.1021/acs.molpharmaceut.5b00942] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Potassium channels are of paramount physiological and pathological importance and therefore constitute significant drug targets. One of the keys to rationalize the way drugs modulate ion channels is to understand the ability of such small molecules to access their respective binding sites, from which they can exert an activating or inhibitory effect. Many computational studies have probed the energetics of ion permeation, and the mechanisms of voltage gating, but little is known about the role of fenestrations as possible mediators of drug entry in potassium channels. To explore the existence, structure, and conformational dynamics of transmembrane fenestrations accessible by drugs in potassium channels, molecular dynamics simulation trajectories were analyzed from three potassium channels: the open state voltage-gated channel Kv1.2, the G protein-gated inward rectifying channel GIRK2 (Kir3.2), and the human two-pore domain TWIK-1 (K2P1.1). The main results of this work were the identification of the sequence identity of four main lateral fenestrations of similar length and with bottleneck radius in the range of 0.9-2.4 Å for this set of potassium channels. It was found that the fenestrations in Kv1.2 and Kir3.2 remain closed to the passage of molecules larger than water. In contrast, in the TWIK-1 channel, both open and closed fenestrations are sampled throughout the simulation, with bottleneck radius shown to correlate with the random entry of lipid membrane molecules into the aperture of the fenestrations. Druggability scoring function analysis of the fenestration regions suggests that Kv and Kir channels studied are not druggable in practice due to steric constraining of the fenestration bottleneck. A high (>50%) fenestration sequence identity was found in each potassium channel subfamily studied, Kv1, Kir3, and K2P1. Finally, the reported fenestration sequence of TWIK-1 compared favorably with another channel, K2P channel TREK-2, reported to possess open fenestrations, suggesting that K2P channels could be druggable via fenestrations, for which we reported atomistic detail of the fenestration region, including the flexible residues M260 and L264 that interact with POPC membrane in a concerted fashion with the aperture and closure of the fenestrations.
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Affiliation(s)
- Christian Jorgensen
- Department of Chemistry, King's College London , Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Leonardo Darré
- Department of Chemistry, King's College London , Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Victoria Oakes
- Department of Chemistry, King's College London , Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Rubben Torella
- Pfizer Neuroscience and Pain Research Unit, Worldwide Medicinal Chemistry , Portway Building, Granta Park, Great Abington, Cambridge CB21 6GS, U.K
| | - David Pryde
- Pfizer Neuroscience and Pain Research Unit, Worldwide Medicinal Chemistry , Portway Building, Granta Park, Great Abington, Cambridge CB21 6GS, U.K
| | - Carmen Domene
- Department of Chemistry, King's College London , Britannia House, 7 Trinity Street, London SE1 1DB, U.K.,Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
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46
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New potential binding determinant for hERG channel inhibitors. Sci Rep 2016; 6:24182. [PMID: 27067805 PMCID: PMC4828713 DOI: 10.1038/srep24182] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/23/2016] [Indexed: 11/08/2022] Open
Abstract
Human ether-à-go-go related gene (hERG) 1 channels conduct the rapid delayed rectifier K+ current (IKr) and are essential for the repolarization of the cardiac action potential. hERG1 inhibition by structurally diverse drugs may lead to life threatening arrhythmia. Putative binding determinants of hERG1 channel blockers include T623, S624 and V625 on the pore helix, and residues G648, Y652 and F656, located on segment S6. We and others have previously hypothesized that additional binding determinants may be located on helix S5, which is in close contact with the S6 segments. In order to test this hypothesis, we performed a detailed investigation combining ionic current measurements with two-microelectrode voltage clamp and molecular modeling techniques. We identified a novel aromatic high affinity binding determinant for blockers located in helix S5, F557, which is equally potent as Y652. Modeling supports a direct interaction with the outer pore helix.
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Linder T, Bernsteiner H, Saxena P, Bauer F, Erker T, Timin E, Hering S, Stary-Weinzinger A. Drug trapping in hERG K + channels: (not) a matter of drug size? MEDCHEMCOMM 2016; 7:512-518. [PMID: 28337337 PMCID: PMC5292991 DOI: 10.1039/c5md00443h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/18/2015] [Indexed: 01/09/2023]
Abstract
Inhibition of hERG K+ channels by structurally diverse drugs prolongs the ventricular action potential and increases the risk of torsade de pointes arrhythmias and sudden cardiac death. The capture of drugs behind closed channel gates, so-called drug trapping, is suggested to harbor an increased pro-arrhythmic risk. In this study, the trapping mechanisms of a trapped hERG blocker propafenone and a bulky derivative (MW: 647.24 g mol-1) were studied by making use of electrophysiological measurements in combination with molecular dynamics simulations. Our study suggests that the hERG cavity is able to accommodate very bulky compounds without disturbing gate closure.
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Affiliation(s)
- Tobias Linder
- Department of Pharmacology and Toxicology , University of Vienna , Austria .
| | - Harald Bernsteiner
- Department of Pharmacology and Toxicology , University of Vienna , Austria .
| | - Priyanka Saxena
- Department of Pharmacology and Toxicology , University of Vienna , Austria .
| | - Florian Bauer
- Department of Pharmaceutical Chemistry , University of Vienna , Austria
| | - Thomas Erker
- Department of Pharmaceutical Chemistry , University of Vienna , Austria
| | - Eugen Timin
- Department of Pharmacology and Toxicology , University of Vienna , Austria .
| | - Steffen Hering
- Department of Pharmacology and Toxicology , University of Vienna , Austria .
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48
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Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, Kolocouris A, Klein ML, Khalid S, Lemieux MJ, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, Bondar AN. Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory. J Membr Biol 2015; 248:611-40. [PMID: 26063070 PMCID: PMC4515176 DOI: 10.1007/s00232-015-9802-0] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/26/2015] [Indexed: 01/05/2023]
Abstract
Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. We present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.
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Affiliation(s)
- Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Toby W. Allen
- School of Applied Sciences & Health Innovations Research Institute, RMIT University, GPO Box 2476, Melbourne, Vic, 3001, Australia; and Department of Chemistry, University of California, Davis. Davis, CA 95616, USA
| | - Ioan Andricioaei
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Bruno Antonny
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 06560 Valbonne, France
| | - Daniel Baum
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Grace Brannigan
- Center for Computational and Integrative Biology and Department of Physics, Rutgers University-Camden, Camden, NJ, USA
| | - Nicolae-Viorel Buchete
- School of Physics and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Lucie Delemotte
- Institute of Computational and Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Coral del Val
- Department of Artificial Intelligence, University of Granada, E-18071 Granada, Spain
| | - Ran Friedman
- Linnæus University, Department of Chemistry and Biomedical Sciences & Centre for Biomaterials Chemistry, 391 82 Kalmar, Sweden
| | - Paraskevi Gkeka
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece
| | - Hans-Christian Hege
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, IBPC and CNRS, Paris, France
| | - Marina A. Kasimova
- Université de Lorraine, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
- Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Antonios Kolocouris
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Athens, Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Michael L. Klein
- Institute of Computational and Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Syma Khalid
- Department of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - M. Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, and Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7
| | - Norbert Lindow
- Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustrasse 7, D-14195 Berlin, Germany
| | - Mahua Roy
- Department of Chemistry, University of California, Irvine
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute), Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Mounir Tarek
- Université de Lorraine, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
- CNRS, SRSMC, UMR 7565, Vandoeuvre-lès-Nancy, F-54500, France
| | - Florentina Tofoleanu
- School of Physics and Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Stefano Vanni
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, UMR 7275, 06560 Valbonne, France
| | - Sinisa Urban
- Johns Hopkins University School of Medicine, Howard Hughes Medical Institute, Department of Molecular Biology & Genetics, 725 N. Wolfe Street, 507 Preclinical Teaching Building, Baltimore, MD 21205, USA
| | - David J. Wales
- University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jeremy C. Smith
- Oak Ridge National Laboratory, PO BOX 2008 MS6309, Oak Ridge, TN 37831-6309, USA
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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