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Qneibi M, Hawash M, Bdir S, Bdair M, Aldwaik SA. Assessing the Effects of Thiazole-Carboxamide Derivatives on the Biophysical Properties of AMPA Receptor Complexes as a Potential Neuroprotective Agent. Molecules 2024; 29:3232. [PMID: 38999182 PMCID: PMC11243149 DOI: 10.3390/molecules29133232] [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: 06/04/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024] Open
Abstract
An optimal balance between excitatory and inhibitory transmission in the central nervous system provides essential neurotransmission for good functioning of the neurons. In the neurology field, a disturbed balance can lead to neurological diseases like epilepsy, Alzheimer's, and Autism. One of the critical agents mediating excitatory neurotransmission is α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptors, which are concerned with synaptic plasticity, memory, and learning. An imbalance in neurotransmission finally results in excitotoxicity and neurological pathologies that should be corrected through specific compounds. Hence, the current study will prove to be an evaluation of new thiazole-carboxamide derivatives concerning AMPAR-modulating activity and extended medicinal potential. In the current project, five previously synthesized thiazole-carboxamide derivatives, i.e., TC-1 to TC-5, were used to interact with the AMPARs expressed in HEK293T cells, which overexpress different subunits of the AMPAR. Patch-clamp analysis was carried out while the effect of the drugs on AMPAR-mediated currents was followed with a particular emphasis on the kinetics of inhibition, desensitization, and deactivation. All tested TC compounds, at all subunits, showed potent inhibition of AMPAR-mediated currents, with TC-2 being the most powerful for all subunits. These compounds shifted the receptor kinetics efficiently, mainly enhancing the deactivation rates, and hence acted as a surrogate for their neuroprotective potentials. Additionally, recently published structure-activity relationship studies identified particular substituent groups as necessary for improving the pharmacologic profiles of these compounds. In this regard, thiazole-carboxamide derivatives, particularly those classified as TC-2, have become essential negative allosteric modulators of AMPAR function and potential therapeutics in neurological disturbances underlain by the dysregulation of excitatory neurotransmission. Given their therapeutic effectiveness and safety profiles, these in vivo studies need to be further validated, although computational modeling can be further developed for drug design and selectivity. This will open possibilities for new drug-like AMPAR negative allosteric modulators with applications at the clinical level toward neurology.
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Affiliation(s)
- Mohammad Qneibi
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus P400, Palestine
| | - Mohammed Hawash
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus P400, Palestine
| | - Sosana Bdir
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus P400, Palestine
| | - Mohammad Bdair
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus P400, Palestine
| | - Samia Ammar Aldwaik
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus P400, Palestine
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2
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Chatterjee N, González-Durruthy M, Costa MD, Ribeiro AR, Vilas-Boas V, Vilasboas-Campos D, Maciel P, Alfaro-Moreno E. Differential impact of diesel exhaust particles on glutamatergic and dopaminergic neurons in Caenorhabditis elegans: A neurodegenerative perspective. ENVIRONMENT INTERNATIONAL 2024; 186:108597. [PMID: 38579453 DOI: 10.1016/j.envint.2024.108597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/29/2024] [Accepted: 03/21/2024] [Indexed: 04/07/2024]
Abstract
The growing body of evidence links exposure to particulate matter pollutants with an increased risk of neurodegenerative diseases. In the present study, we investigated whether diesel exhaust particles can induce neurobehavioral alterations associated with neurodegenerative effects on glutamatergic and dopaminergic neurons in Caenorhabditis elegans (C. elegans). Exposure to DEP at concentrations of 0.167 µg/cm2 and 1.67 µg/cm2 resulted in significant developmental delays and altered locomotion behaviour. These effects were accompanied by discernible alterations in the expressions of antioxidant genes sod-3 and gst-4 observed in transgenic strains. Behaviour analysis demonstrated a significant reduction in average speed (p < 0.001), altered paths, and decreased swimming activities (p < 0.01), particularly at mid and high doses. Subsequent assessment of neurodegeneration markers in glutamatergic (DA1240) and dopaminergic (BZ555) transgenic worms revealed notable glutamatergic neuron degeneration at 0.167 μg/cm2 (∼30 % moderate, ∼20 % advanced) and 1.67 μg/cm2 (∼28 % moderate, ∼24 % advanced, p < 0.0001), while dopaminergic neurons exhibited structural deformities (∼16 %) without significant degeneration in terms of blebs and breaks. Furthermore, in silico docking simulations suggest the presence of an antagonistic competitive inhibition induced by DEP in the evaluated neuro-targets, stronger for the glutamatergic transporter than for the dopaminergic receptor from the comparative binding affinity point of view. The results underscore DEP's distinctive neurodegenerative effects and suggest a link between locomotion defects and glutamatergic neurodegeneration in C. elegans, providing insights into environmental health risks assessment.
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Affiliation(s)
- Nivedita Chatterjee
- NanoSafety Group, International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal.
| | | | - Marta Daniela Costa
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimaraes, Portugal
| | - Ana R Ribeiro
- NanoSafety Group, International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal
| | - Vânia Vilas-Boas
- NanoSafety Group, International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal
| | - Daniela Vilasboas-Campos
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimaraes, Portugal
| | - Patrícia Maciel
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimaraes, Portugal
| | - Ernesto Alfaro-Moreno
- NanoSafety Group, International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal.
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Nieoczym D, Marszalek-Grabska M, Szalak R, Kundap U, Kaczor AA, Wrobel TM, Kosheva N, Komar M, Abram M, Esguerra CV, Samarut E, Pieróg M, Jakubiec M, Kaminski K, Kukula-Koch W, Gawel K. A comprehensive assessment of palmatine as anticonvulsant agent - In vivo and in silico studies. Biomed Pharmacother 2024; 172:116234. [PMID: 38325264 DOI: 10.1016/j.biopha.2024.116234] [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: 11/08/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/09/2024] Open
Abstract
Previously, we demonstrated that palmatine (PALM) - an isoquinoline alkaloid from Berberis sibrica radix, exerted antiseizure activity in the pentylenetetrazole (PTZ)-induced seizure assay in larval zebrafish. The aim of the present study was to more precisely characterize PALM as a potential anticonvulsant drug candidate. A range of zebrafish and mouse seizure/epilepsy models were applied in the investigation. Immunostaining analysis was conducted to assess the changes in mouse brains, while in silico molecular modelling was performed to determine potential targets for PALM. Accordingly, PALM had anticonvulsant effect in ethyl 2-ketopent-4-enoate (EKP)-induced seizure assay in zebrafish larvae as well as in the 6 Hz-induced psychomotor seizure threshold and timed infusion PTZ tests in mice. The protective effect in the EKP-induced seizure assay was confirmed in the local field potential recordings. PALM did not affect seizures in the gabra1a knockout line of zebrafish larvae. In the scn1Lab-/- zebrafish line, pretreatment with PALM potentiated seizure-like behaviour of larvae. Repetitive treatment with PALM, however, did not reduce development of PTZ-induced seizure activity nor prevent the loss of parvalbumin-interneurons in the hippocampus of the PTZ kindled mice. In silico molecular modelling revealed that the noted anticonvulsant effect of PALM in EKP-induced seizure assay might result from its interactions with glutamic acid decarboxylase and/or via AMPA receptor non-competitive antagonism. Our study has demonstrated the anticonvulsant activity of PALM in some experimental models of seizures, including a model of pharmacoresistant seizures induced by EKP. These results indicate that PALM might be a suitable new drug candidate but the precise mechanism of its anticonvulsant activity has to be determined.
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Affiliation(s)
- Dorota Nieoczym
- Chair of Animal Physiology and Pharmacology, Institute of Biology and Biochemistry, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka Str. 19, 20-033 Lublin, Poland
| | - Marta Marszalek-Grabska
- Department of Experimental and Clinical Pharmacology, Medical University of Lublin, Jaczewskiego Str. 8b, 20-090 Lublin, Poland
| | - Radoslaw Szalak
- Department of Animal Anatomy and Histology, Faculty of Veterinary Medicine, University of Life Sciences, 12 Akademicka St., 20-950 Lublin, Poland
| | - Uday Kundap
- Research Center of the University of Montreal Hospital Center (CRCHUM), Department of Neurosciences, Université de Montréal, Montréal, QC H2X 0A9, Canada; Canada East Spine Centre, Saint John Regional Hospital, Department of Spine and Orthopaedics surgery, Horizon Health Network, Saint John, NB E2L 4L4, Canada
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodżki St., PL-20093 Lublin, Poland; School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Tomasz M Wrobel
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodżki St., PL-20093 Lublin, Poland
| | - Nataliia Kosheva
- Department of Experimental and Clinical Pharmacology, Medical University of Lublin, Jaczewskiego Str. 8b, 20-090 Lublin, Poland
| | - Malgorzata Komar
- Department of Animal Anatomy and Histology, Faculty of Veterinary Medicine, University of Life Sciences, 12 Akademicka St., 20-950 Lublin, Poland
| | - Michal Abram
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Cracow, Poland
| | - Camila V Esguerra
- Chemical Neuroscience Group, Centre for Molecular Medicine Norway, University of Oslo, Gaustadalleen 21, Forskningsparken, 0349 Oslo, Norway
| | - Eric Samarut
- Research Center of the University of Montreal Hospital Center (CRCHUM), Department of Neurosciences, Université de Montréal, Montréal, QC H2X 0A9, Canada; Neurosciences Department, University of Montreal, Montreal, QC, Canada
| | - Mateusz Pieróg
- Chair of Animal Physiology and Pharmacology, Institute of Biology and Biochemistry, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka Str. 19, 20-033 Lublin, Poland
| | - Marcin Jakubiec
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Cracow, Poland
| | - Krzysztof Kaminski
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Cracow, Poland
| | - Wirginia Kukula-Koch
- Department of Pharmacognosy with Medicinal Plants Garden, Medical University of Lublin, Chodzki Str. 1, 20-093 Lublin, Poland
| | - Kinga Gawel
- Department of Experimental and Clinical Pharmacology, Medical University of Lublin, Jaczewskiego Str. 8b, 20-090 Lublin, Poland.
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Qneibi M, Bdir S, Bdair M, Aldwaik SA, Sandouka D, Heeh M, Idais TI. AMPA receptor neurotransmission and therapeutic applications: A comprehensive review of their multifaceted modulation. Eur J Med Chem 2024; 266:116151. [PMID: 38237342 DOI: 10.1016/j.ejmech.2024.116151] [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: 12/14/2023] [Revised: 01/02/2024] [Accepted: 01/11/2024] [Indexed: 02/05/2024]
Abstract
The neuropharmacological community has shown a strong interest in AMPA receptors as critical components of excitatory synaptic transmission during the last fifteen years. AMPA receptors, members of the ionotropic glutamate receptor family, allow rapid excitatory neurotransmission in the brain. AMPA receptors, which are permeable to sodium and potassium ions, manage the bulk of the brain's rapid synaptic communications. This study thoroughly examines the recent developments in AMPA receptor regulation, focusing on a shift from single chemical illustrations to a more extensive investigation of underlying processes. The complex interplay of these modulators in modifying the function and structure of AMPA receptors is the main focus, providing insight into their influence on the speed of excitatory neurotransmission. This research emphasizes the potential of AMPA receptor modulation as a therapy for various neurological disorders such as epilepsy and Alzheimer's disease. Analyzing these regulators' sophisticated molecular details enhances our comprehension of neuropharmacology, representing a significant advancement in using AMPA receptors for treating intricate neurological conditions.
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Affiliation(s)
- Mohammad Qneibi
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine.
| | - Sosana Bdir
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Mohammad Bdair
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Samia Ammar Aldwaik
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Dana Sandouka
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | | | - Tala Iyad Idais
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
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5
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Golubeva EA, Lavrov MI, Radchenko EV, Palyulin VA. Diversity of AMPA Receptor Ligands: Chemotypes, Binding Modes, Mechanisms of Action, and Therapeutic Effects. Biomolecules 2022; 13:biom13010056. [PMID: 36671441 PMCID: PMC9856200 DOI: 10.3390/biom13010056] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
L-Glutamic acid is the main excitatory neurotransmitter in the central nervous system (CNS). Its associated receptors localized on neuronal and non-neuronal cells mediate rapid excitatory synaptic transmission in the CNS and regulate a wide range of processes in the brain, spinal cord, retina, and peripheral nervous system. In particular, the glutamate receptors selective to α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) also play an important role in numerous neurological disorders and attract close attention as targets for the creation of new classes of drugs for the treatment or substantial correction of a number of serious neurodegenerative and neuropsychiatric diseases. For this reason, the search for various types of AMPA receptor ligands and studies of their properties are attracting considerable attention both in academic institutions and in pharmaceutical companies around the world. This review focuses mainly on the advances in this area published since 2017. Particular attention is paid to the structural diversity of new chemotypes of agonists, competitive AMPA receptor antagonists, positive and negative allosteric modulators, transmembrane AMPA regulatory protein (TARP) dependent allosteric modulators, ion channel blockers as well as their binding sites. This review also presents the studies of the mechanisms of action of AMPA receptor ligands that mediate their therapeutic effects.
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6
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Lavrov MI, Veremeeva PN, Golubeva EA, Radchenko EV, Zamoyski VL, Grigoriev VV, Palyulin VA. Positive and negative AMPA receptor modulators based on tricyclic bispidine derivative: Minor structural change inverts the type of activity. MENDELEEV COMMUNICATIONS 2022. [DOI: 10.1016/j.mencom.2022.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Herguedas B, Kohegyi BK, Dohrke JN, Watson JF, Zhang D, Ho H, Shaikh SA, Lape R, Krieger JM, Greger IH. Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. Nat Commun 2022; 13:734. [PMID: 35136046 PMCID: PMC8826358 DOI: 10.1038/s41467-022-28404-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/13/2022] [Indexed: 01/01/2023] Open
Abstract
AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory synapses in the brain. Glutamate binding to the receptor’s ligand-binding domains (LBDs) leads to ion channel activation and desensitization. Gating kinetics shape synaptic transmission and are strongly modulated by transmembrane AMPAR regulatory proteins (TARPs) through currently incompletely resolved mechanisms. Here, electron cryo-microscopy structures of the GluA1/2 TARP-γ8 complex, in both open and desensitized states (at 3.5 Å), reveal state-selective engagement of the LBDs by the large TARP-γ8 loop (‘β1’), elucidating how this TARP stabilizes specific gating states. We further show how TARPs alter channel rectification, by interacting with the pore helix of the selectivity filter. Lastly, we reveal that the Q/R-editing site couples the channel constriction at the filter entrance to the gate, and forms the major cation binding site in the conduction path. Our results provide a mechanistic framework of how TARPs modulate AMPAR gating and conductance. AMPA glutamate receptors, mediate the majority of excitatory signaling in the brain. Here the authors show how the auxiliary subunit TARP-γ8 shapes gating kinetics, ion conductance and rectification properties of the heteromeric GluA1/2 AMPA receptor.
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Affiliation(s)
- Beatriz Herguedas
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK.,Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, 50018, Zaragoza, Spain
| | - Bianka K Kohegyi
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jan-Niklas Dohrke
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK.,Universitätsmedizin Göttingen, Georg-August-Universität, 37075, Göttingen, Germany
| | - Jake F Watson
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK.,Institute of Science and Technology (IST) Austria, Am Campus 1, 3400, Klosterneuburg, Austria
| | - Danyang Zhang
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Hinze Ho
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Physiological Laboratory, Cambridge, UK
| | - Saher A Shaikh
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Remigijus Lape
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK
| | - James M Krieger
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Ingo H Greger
- Neurobiology Division MRC Laboratory of Molecular Biology, Cambridge, UK.
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Radchenko EV, Tarakanova AS, Karlov DS, Lavrov MI, Palyulin VA. [Ligands of the AMPA-subtype glutamate receptors: mechanisms of action and novel chemotypes]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2021; 67:187-200. [PMID: 34142526 DOI: 10.18097/pbmc20216703187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ionotropic glutamate receptors of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) subtype play a key role in synaptic plasticity representing one of the mechanisms for learning and memory formation. They can also serve as targets for the development of novel classes of pharmaceuticals for the treatment or substantive correction of many serious neurodegenerative and psychoneurological disorders. The search and studies of various types of AMPA receptor ligands attract considerable attention from academic organizations and pharmaceutical companies all over the world. This review mainly focuses on recent advances in this field. The architecture and operational mechanism of the receptor as well as its major binding sites and ligand types are considered. Special attention is paid to the studies of mechanisms of action and novel chemotypes of AMPA receptor agonists and competitive antagonists, positive and negative allosteric modulators, auxiliary protein-dependent allosteric modulators, and ion channel blockers.
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Affiliation(s)
| | | | - D S Karlov
- Lomonosov Moscow State University, Moscow, Russia
| | - M I Lavrov
- Lomonosov Moscow State University, Moscow, Russia
| | - V A Palyulin
- Lomonosov Moscow State University, Moscow, Russia
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9
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Han Y, Wang Z, Ren J, Wei Z, Li J. Potential inhibitors for the novel coronavirus (SARS-CoV-2). Brief Bioinform 2021; 22:1225-1231. [PMID: 32942296 PMCID: PMC7543260 DOI: 10.1093/bib/bbaa209] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/27/2020] [Accepted: 08/12/2020] [Indexed: 01/03/2023] Open
Abstract
The lack of a vaccine or any effective treatment for the aggressive novel coronavirus disease (COVID-19) has created a sense of urgency for the discovery of effective drugs. Several repurposing pharmaceutical candidates have been reported or envisaged to inhibit the emerging infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but their binding sites, binding affinities and inhibitory mechanisms are still unavailable. In this study, we use the ligand-protein docking program and molecular dynamic simulation to ab initio investigate the binding mechanism and inhibitory ability of seven clinically approved drugs (Chloroquine, Hydroxychloroquine, Remdesivir, Ritonavir, Beclabuvir, Indinavir and Favipiravir) and a recently designed α-ketoamide inhibitor (13b) at the molecular level. The results suggest that Chloroquine has the strongest binding affinity with 3CL hydrolase (Mpro) among clinically approved drugs, indicating its effective inhibitory ability for SARS-CoV-2. However, the newly designed inhibitor 13b shows potentially improved inhibition efficiency with larger binding energy compared with Chloroquine. We further calculate the important binding site residues at the active site and demonstrate that the MET 165 and HIE 163 contribute the most for 13b, while the MET 165 and GLN 189 for Chloroquine, based on residual energy decomposition analysis. The proposed work offers a higher research priority for 13b to treat the infection of SARS-CoV-2 and provides theoretical basis for further design of effective drug molecules with stronger inhibition.
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Affiliation(s)
| | | | - Jiahao Ren
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine
| | - Zhiyun Wei
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication; Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University
| | - Jinjin Li
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Shanghai Jiao Tong University, Shanghai, 200240, China
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