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Zlobin A, Smirnov I, Golovin A. Dynamic interchange between two protonation states is characteristic of active sites of cholinesterases. Protein Sci 2024; 33:e5100. [PMID: 39022909 PMCID: PMC11255601 DOI: 10.1002/pro.5100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/28/2024] [Accepted: 06/19/2024] [Indexed: 07/20/2024]
Abstract
Cholinesterases are well-known and widely studied enzymes crucial to human health and involved in neurology, Alzheimer's, and lipid metabolism. The protonation pattern of active sites of cholinesterases influences all the chemical processes within, including reaction, covalent inhibition by nerve agents, and reactivation. Despite its significance, our comprehension of the fine structure of cholinesterases remains limited. In this study, we employed enhanced-sampling quantum-mechanical/molecular-mechanical calculations to show that cholinesterases predominantly operate as dynamic mixtures of two protonation states. The proton transfer between two non-catalytic glutamate residues follows the Grotthuss mechanism facilitated by a mediator water molecule. We show that this uncovered complexity of active sites presents a challenge for classical molecular dynamics simulations and calls for special treatment. The calculated proton transfer barrier of 1.65 kcal/mol initiates a discussion on the potential existence of two coupled low-barrier hydrogen bonds in the inhibited form of butyrylcholinesterase. These findings expand our understanding of structural features expressed by highly evolved enzymes and guide future advances in cholinesterase-related protein and drug design studies.
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Affiliation(s)
- Alexander Zlobin
- Institute for Drug DiscoveryLeipzig University Medical SchoolLeipzigGermany
- Faculty of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
| | - Ivan Smirnov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussia
| | - Andrey Golovin
- Faculty of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscowRussia
- Belozersky Institute of Physico‐Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
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Ramírez-Ruiz AM, Ávila-Cossío ME, Estolano-Cobián A, Cornejo-Bravo JM, Martinez AL, Córdova-Guerrero I, Cota-Ramírez BR, Carranza-Ambriz KP, Rivero IA, Serrano-Medina A. Inhibitory Activity of 4-Benzylidene Oxazolones Derivatives of Cinnamic Acid on Human Acetylcholinesterase and Cognitive Improvements in a Mouse Model. Molecules 2023; 28:7392. [PMID: 37959813 PMCID: PMC10649417 DOI: 10.3390/molecules28217392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
We synthesized seven (Z)-benzylidene-2-(E)-styryloxazol-5(4H)-ones derivatives of cinnamic acid and evaluated the ability of these compounds to inhibit human acetylcholinesterase (hAChE). The most potent compound was evaluated for cognitive improvement in short-term memory. The seven compounds reversibly inhibited the hAChE between 51 and 75% at 300 μM, showed an affinity (Ki) from 2 to 198 μM, and an IC50 from 9 to 246 μM. Molecular docking studies revealed that all binding moieties are involved in the non-covalent interactions with hAChE for all compounds. In addition, in silico pharmacokinetic analysis was carried out to predict the compounds' blood-brain barrier (BBB) permeability. The most potent inhibitor of hAChE significantly improved cognitive impairment in a modified Y-maze test (5 μmol/kg) and an Object Recognition Test (10 μmol/kg). Our results can help the rational design of hAChE inhibitors to work as potential candidates for treating cognitive disorders.
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Affiliation(s)
- Alma Marisol Ramírez-Ruiz
- Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico (A.L.M.); (K.P.C.-A.)
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico; (A.E.-C.); (J.M.C.-B.); (I.C.-G.); (B.R.C.-R.)
| | - Martha Elena Ávila-Cossío
- Centro de Graduados e Investigación en Química, Tecnológico Nacional de Mexico/Instituto Tecnológico de Tijuana, Tijuana 22510, BC, Mexico;
| | - Arturo Estolano-Cobián
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico; (A.E.-C.); (J.M.C.-B.); (I.C.-G.); (B.R.C.-R.)
| | - José Manuel Cornejo-Bravo
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico; (A.E.-C.); (J.M.C.-B.); (I.C.-G.); (B.R.C.-R.)
| | - Ana Laura Martinez
- Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico (A.L.M.); (K.P.C.-A.)
| | - Iván Córdova-Guerrero
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico; (A.E.-C.); (J.M.C.-B.); (I.C.-G.); (B.R.C.-R.)
| | - Bibiana Roselly Cota-Ramírez
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico; (A.E.-C.); (J.M.C.-B.); (I.C.-G.); (B.R.C.-R.)
| | - Krysta Paola Carranza-Ambriz
- Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico (A.L.M.); (K.P.C.-A.)
| | - Ignacio A. Rivero
- Centro de Graduados e Investigación en Química, Tecnológico Nacional de Mexico/Instituto Tecnológico de Tijuana, Tijuana 22510, BC, Mexico;
| | - Aracely Serrano-Medina
- Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico (A.L.M.); (K.P.C.-A.)
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico; (A.E.-C.); (J.M.C.-B.); (I.C.-G.); (B.R.C.-R.)
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Mukhametgalieva AR, Nemtarev AV, Sykaev VV, Pashirova TN, Masson P. Activation/Inhibition of Cholinesterases by Excess Substrate: Interpretation of the Phenomenological b Factor in Steady-State Rate Equation. Int J Mol Sci 2023; 24:10472. [PMID: 37445649 DOI: 10.3390/ijms241310472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Cholinesterases (ChEs) display a non-michaelian behavior with positively charged substrates. In the steady-state rate equation, the b factor describes this behavior: if b > 1 there is substrate activation, if b < 1 there is substrate inhibition. The mechanistic significance of the b factor was investigated to determine whether this behavior depends on acylation, deacylation or on both steps. Kinetics of human acetyl- (AChE) and butyryl-cholinesterase (BChE) were performed under steady-state conditions and using a time-course of complete substrate hydrolysis. For the hydrolysis of short acyl(thio)esters, where acylation and deacylation are partly rate-limiting, steady-state kinetic analysis could not decide which step determines b. However, the study of the hydrolysis of an arylacylamide, 3-(acetamido)-N,N,N-trimethylanilinium (ATMA), where acetylation is rate-limiting, showed that b depends on the acylation step. The magnitude of b and opposite b values between AChE and BChE for the hydrolysis of acetyl(thio)- versus benzoyl-(thio) esters, then indicated that the productive adjustment of substrates in the active center at high concentration depends on motions of both the Ω and the acyl-binding loops. Benzoylcholine was shown to be a poor substrate of AChE, and steady-state kinetics showed a sudden inhibition at high concentration, likely due to the non-dissociation of hydrolysis products. The poor catalytic hydrolysis of this bulky ester by AChE illustrates the importance of the fine adjustment of substrate acyl moiety in the acyl-binding pocket. Molecular modeling and QM/MM simulations should definitively provide evidence for this statement.
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Affiliation(s)
- Aliya R Mukhametgalieva
- Biochemical Neuropharmacology Laboratory, Kazan Federal University, 18 Ul. Kremlevskaya, 420008 Kazan, Russia
| | - Andrey V Nemtarev
- Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 8 Ul. Arbuzov, 420088 Kazan, Russia
| | - Viktor V Sykaev
- Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 8 Ul. Arbuzov, 420088 Kazan, Russia
| | - Tatiana N Pashirova
- Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 8 Ul. Arbuzov, 420088 Kazan, Russia
| | - Patrick Masson
- Biochemical Neuropharmacology Laboratory, Kazan Federal University, 18 Ul. Kremlevskaya, 420008 Kazan, Russia
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Gerlits O, Fajer M, Cheng X, Blumenthal DK, Radić Z, Kovalevsky A. Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X-ray crystallography and inelastic neutron scattering. Structure 2022; 30:1538-1549.e3. [PMID: 36265484 PMCID: PMC9637784 DOI: 10.1016/j.str.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/07/2022] [Accepted: 09/25/2022] [Indexed: 11/06/2022]
Abstract
Organophosphorus (OP) compounds, including nerve agents and some pesticides, covalently bind to the catalytic serine of human acetylcholinesterase (hAChE), thereby inhibiting acetylcholine hydrolysis necessary for efficient neurotransmission. Oxime antidotes can reactivate the OP-conjugated hAChE, but reactivation efficiency can be low for pesticides, such as paraoxon (POX). Understanding structural and dynamic determinants of OP inhibition and reactivation can provide insights to design improved reactivators. Here, X-ray structures of hAChE with unaged POX, with POX and oximes MMB4 and RS170B, and with MMB4 are reported. A significant conformational distortion of the acyl loop was observed upon POX binding, being partially restored to the native conformation by oximes. Neutron vibrational spectroscopy combined with molecular dynamics simulations showed that picosecond vibrational dynamics of the acyl loop soften in the ∼20-50 cm-1 frequency range. The acyl loop structural perturbations may be correlated with its picosecond vibrational dynamics to yield more comprehensive template for structure-based reactivator design.
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Affiliation(s)
- Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN 37303, USA
| | - Mikolai Fajer
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaolin Cheng
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Donald K Blumenthal
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA
| | - Zoran Radić
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093-0657, USA.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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