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Habiballah S, Chambers J, Meek E, Reisfeld B. The in silico identification of novel broad-spectrum antidotes for poisoning by organophosphate anticholinesterases. J Comput Aided Mol Des 2023; 37:755-764. [PMID: 37796381 PMCID: PMC11251483 DOI: 10.1007/s10822-023-00537-x] [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: 07/12/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023]
Abstract
Owing to their potential to cause serious adverse health effects, significant efforts have been made to develop antidotes for organophosphate (OP) anticholinesterases, such as nerve agents. To be optimally effective, antidotes must not only reactivate inhibited target enzymes, but also have the ability to cross the blood-brain barrier (BBB). Progress has been made toward brain-penetrating acetylcholinesterase reactivators through the development of a new group of substituted phenoxyalkyl pyridinium oximes. To help in the selection and prioritization of compounds for future synthesis and testing within this class of chemicals, and to identify candidate broad-spectrum molecules, an in silico framework was developed to systematically generate structures and screen them for reactivation efficacy and BBB penetration potential.
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Affiliation(s)
- Sohaib Habiballah
- Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO, 80523-1370, USA
| | - Janice Chambers
- Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, 240 Wise Center Drive, Mississippi State, MS, 39762-6100, USA
| | - Edward Meek
- Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, 240 Wise Center Drive, Mississippi State, MS, 39762-6100, USA
| | - Brad Reisfeld
- Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, CO, 80523-1370, USA.
- Colorado School of Public Health, Colorado State University, 1612 Campus Delivery, Fort Collins, CO, 80523-1612, USA.
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2
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Habiballah S, Chambers J, Meek E, Reisfeld B. The in silico identification of novel broad-spectrum antidotes for poisoning by organophosphate anticholinesterases. RESEARCH SQUARE 2023:rs.3.rs-3163943. [PMID: 37502931 PMCID: PMC10371142 DOI: 10.21203/rs.3.rs-3163943/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Because of their potential to cause serious adverse health effects, significant efforts have been made to develop antidotes for organophosphate (OP) anticholinesterases, such as nerve agents. To be optimally effective, antidotes must not only reactivate inhibited target enzymes, but also have the ability to cross the blood brain barrier (BBB). Progress has been made toward brain-penetrating acetylcholinesterase reactivators through the development of a new group of substituted phenoxyalkyl pyridinium oximes. To help in the selection and prioritization of compounds for future synthesis and testing within this class of chemicals, and to identify candidate broad-spectrum molecules, an in silico framework was developed to systematically generate structures and screen them for reactivation efficacy and BBB penetration potential.
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Affiliation(s)
- Sohaib Habiballah
- Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, 80523-1370, CO, USA
| | - Janice Chambers
- Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, 240 Wise Center Drive, Mississippi State, 39762-6100, MS, USA
| | - Edward Meek
- Center for Environmental Health Sciences, College of Veterinary Medicine, Mississippi State University, 240 Wise Center Drive, Mississippi State, 39762-6100, MS, USA
| | - Brad Reisfeld
- Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort Collins, 80523-1370, CO, USA
- Colorado School of Public Health, Colorado State University, 1612 Campus Delivery, Fort Collins, 80523-1612, CO, USA
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3
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Lindgren C, Forsgren N, Hoster N, Akfur C, Artursson E, Edvinsson L, Svensson R, Worek F, Ekström F, Linusson A. Broad-Spectrum Antidote Discovery by Untangling the Reactivation Mechanism of Nerve-Agent-Inhibited Acetylcholinesterase. Chemistry 2022; 28:e202200678. [PMID: 35420233 PMCID: PMC9400889 DOI: 10.1002/chem.202200678] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Indexed: 11/13/2022]
Abstract
Reactivators are vital for the treatment of organophosphorus nerve agent (OPNA) intoxication but new alternatives are needed due to their limited clinical applicability. The toxicity of OPNAs stems from covalent inhibition of the essential enzyme acetylcholinesterase (AChE), which reactivators relieve via a chemical reaction with the inactivated enzyme. Here, we present new strategies and tools for developing reactivators. We discover suitable inhibitor scaffolds by using an activity-independent competition assay to study non-covalent interactions with OPNA-AChEs and transform these inhibitors into broad-spectrum reactivators. Moreover, we identify determinants of reactivation efficiency by analysing reactivation and pre-reactivation kinetics together with structural data. Our results show that new OPNA reactivators can be discovered rationally by exploiting detailed knowledge of the reactivation mechanism of OPNA-inhibited AChE.
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Affiliation(s)
| | - Nina Forsgren
- CBRN Defense and SecuritySwedish Defense Research Agency906 21UmeåSweden
| | - Norman Hoster
- Department of ChemistryUmeå University901 87UmeåSweden
| | - Christine Akfur
- CBRN Defense and SecuritySwedish Defense Research Agency906 21UmeåSweden
| | - Elisabet Artursson
- CBRN Defense and SecuritySwedish Defense Research Agency906 21UmeåSweden
| | | | | | - Franz Worek
- Bundeswehr Institute of Pharmacology and Toxicology80937MunichGermany
| | - Fredrik Ekström
- CBRN Defense and SecuritySwedish Defense Research Agency906 21UmeåSweden
| | - Anna Linusson
- Department of ChemistryUmeå University901 87UmeåSweden
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Odenkirk MT, Reif DM, Baker ES. Multiomic Big Data Analysis Challenges: Increasing Confidence in the Interpretation of Artificial Intelligence Assessments. Anal Chem 2021; 93:7763-7773. [PMID: 34029068 PMCID: PMC8465926 DOI: 10.1021/acs.analchem.0c04850] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The need for holistic molecular measurements to better understand disease initiation, development, diagnosis, and therapy has led to an increasing number of multiomic analyses. The wealth of information available from multiomic assessments, however, requires both the evaluation and interpretation of extremely large data sets, limiting analysis throughput and ease of adoption. Computational methods utilizing artificial intelligence (AI) provide the most promising way to address these challenges, yet despite the conceptual benefits of AI and its successful application in singular omic studies, the widespread use of AI in multiomic studies remains limited. Here, we discuss present and future capabilities of AI techniques in multiomic studies while introducing analytical checks and balances to validate the computational conclusions.
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Affiliation(s)
- Melanie T Odenkirk
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - David M Reif
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27606, United States
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, United States
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5
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Influence of gauche effect on uncharged oxime reactivators for the reactivation of tabun-inhibited AChE: quantum chemical and steered molecular dynamics studies. J Comput Aided Mol Des 2018; 32:793-807. [DOI: 10.1007/s10822-018-0130-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/04/2018] [Indexed: 02/06/2023]
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Driant T, Nachon F, Ollivier C, Renard PY, Derat E. On the Influence of the Protonation States of Active Site Residues on AChE Reactivation: A QM/MM Approach. Chembiochem 2017; 18:666-675. [PMID: 28106328 DOI: 10.1002/cbic.201600646] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Indexed: 11/10/2022]
Abstract
Acetylcholinesterase (AChE), an enzyme of the serine hydrolase superfamily, is a mediator of signal transmission at cholinergic synapses by catalyzing acetylcholine cleavage into acetate and choline. This enzyme is vulnerable to covalent inhibition by organophosphate compounds (like VX). Covalent inhibition of AChE does not revert spontaneously. Known reactivator compounds have limited action in restoring catalytic activity. QM/MM simulations of VX-inhibited AChE reactivation by pralidoxime (2-PAM), a classical reactivator, were performed. These afforded a broad view of the effect of protonation states of active-site residues, and provide evidence for the role of Glu202, which needs to be protonated for reactivation to occur. In situ deprotonation of 2-PAM for both protonation states of Glu202 showed that His447 is able to deprotonate 2-PAM with the assistance of Glu202. Because the active site of serine hydrolases is highly conserved, this work provides new insights on the interplay between the catalytic triad residues and this glutamate, newly identified as protonatable.
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Affiliation(s)
- Thomas Driant
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Florian Nachon
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, 1 Place Général Valérie André, 91223, Brétigny-sur-Orge Cédex, France
| | - Cyril Ollivier
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Pierre-Yves Renard
- Normandie Université, COBRA, UMR 6014 and FR 3038, Université Rouen-Normandie, INSA Rouen, CNRS, 1 rue Tesnière, 76821, Mont-Saint-Aignan Cedex, France
| | - Etienne Derat
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
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Lo R, Ganguly B. Can hydroxylamine be a more potent nucleophile for the reactivation of tabun-inhibited AChE than prototype oxime drugs? An answer derived from quantum chemical and steered molecular dynamics studies. MOLECULAR BIOSYSTEMS 2015; 10:2368-83. [PMID: 24964273 DOI: 10.1039/c4mb00083h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Organophosphorus nerve agents are highly toxic compounds which strongly inhibit acetylcholinesterase (AChE) in the blood and in the central nervous system (CNS). Tabun is one of the highly toxic organophosphorus (OP) compounds and is resistant to many oxime drugs formulated for the reactivation of AChE. The reactivation mechanism of tabun-conjugated AChE with various drugs has been examined with density functional theory and ab initio quantum chemical calculations. The presence of a lone-pair located on the amidic group resists the nucleophilic attack at the phosphorus center of the tabun-conjugated AChE. We have shown that the newly designed drug candidate N-(pyridin-2-yl)hydroxylamine, at the MP2/6-31+G*//M05-2X/6-31G* level in the aqueous phase with the polarizable continuum solvation model (PCM), is more effective in reactivating the tabun-conjugated AChE than typical oxime drugs. The rate determining activation barrier with N-(pyridin-2-yl)hydroxylamine was found to be ∼1.7 kcal mol(-1), which is 7.2 kcal mol(-1) lower than the charged oxime trimedoxime (one of the most efficient reactivators in tabun poisonings). The greater nucleophilicity index (ω(-)) and higher CHelpG charge of pyridinylhydroxylamine compared to TMB4 support this observation. Furthermore, we have also examined the reactivation process of tabun-inhibited AChE with some other bis-quaternary oxime drug candidates such as methoxime (MMB4) and obidoxime. The docking analysis suggests that charged bis-quaternary pyridinium oximes have greater binding affinity inside the active-site gorge of AChE compared to the neutral pyridinylhydroxylamine. The peripheral ligand attached to the neutral pyridinylhydroxylamine enhanced the binding with the aromatic residues in the active-site gorge of AChE through effective π-π interactions. Steered molecular dynamics (SMD) simulations have also been performed with the charged oxime (TMB4) and the neutral hydroxylamine. From protein-drug interaction parameters (rupture force profiles, hydrogen bonds, hydrophobic interactions), geometry and the orientation of the drug candidates, the hydroxylamine is suggested to orchestrate the reactivation process better than TMB4. Furthermore, the calculated log P values show the effective penetration of the neutral drug candidate through the blood-brain barrier. The toxicity measurements and the IC50 values (a measure of the intrinsic affinity toward AChE) suggest that the pyridinylhydroxylamine compound could have similar toxic behavior compared to the prototype oxime antidotes used for reactivation purposes. The newly designed pyridinylhydroxylamine drug candidate can be an effective antidote both kinetically and structurally to reactivate the tabun-inhibited enzyme.
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Affiliation(s)
- Rabindranath Lo
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, India-364 002.
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Chandar NB, Lo R, Kesharwani MK, Ganguly B. In silico study on aging and reactivation processes of tabun conjugated AChE. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00497c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study revealed that the reactivation of tabun inhibited AChE is feasible with neutral antidotes prior to the aging process.
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Affiliation(s)
- Nellore Bhanu Chandar
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR-Central Salt & Marine Chemicals Research Institute
- Bhavnagar
- India-364 002
- Academy of Scientific and Innovative Research
| | - Rabindranath Lo
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR-Central Salt & Marine Chemicals Research Institute
- Bhavnagar
- India-364 002
| | - Manoj K. Kesharwani
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR-Central Salt & Marine Chemicals Research Institute
- Bhavnagar
- India-364 002
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR-Central Salt & Marine Chemicals Research Institute
- Bhavnagar
- India-364 002
- Academy of Scientific and Innovative Research
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Kassa J, Sepsova V, Tumova M, Horova A, Musilek K. A Comparison of the Reactivating and Therapeutic Efficacy of Two Newly Developed Oximes (K727 and K733) with Oxime K203 and Trimedoxime in Tabun-Poisoned Rats and Mice. Basic Clin Pharmacol Toxicol 2014; 116:367-71. [DOI: 10.1111/bcpt.12327] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/08/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Jiri Kassa
- Department of Toxicology and Military Pharmacy; Faculty of Military Health Sciences; Hradec Kralove Czech Republic
| | - Vendula Sepsova
- Department of Toxicology and Military Pharmacy; Faculty of Military Health Sciences; Hradec Kralove Czech Republic
| | - Martina Tumova
- Department of Toxicology and Military Pharmacy; Faculty of Military Health Sciences; Hradec Kralove Czech Republic
| | - Anna Horova
- Department of Toxicology and Military Pharmacy; Faculty of Military Health Sciences; Hradec Kralove Czech Republic
| | - Kamil Musilek
- Department of Toxicology and Military Pharmacy; Faculty of Military Health Sciences; Hradec Kralove Czech Republic
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Quantum chemical and steered molecular dynamics studies for one pot solution to reactivate aged acetylcholinesterase with alkylator oxime. Chem Biol Interact 2014; 223:58-68. [PMID: 25218671 DOI: 10.1016/j.cbi.2014.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/30/2014] [Accepted: 08/29/2014] [Indexed: 11/23/2022]
Abstract
Dimethyl(pyridin-2-yl)sulfonium based oxime has been designed to reverse the aging process of organophosphorus inhibited AChE and to reactivate the aged-AChE adduct. We have employed DFT M05-2X/6-31G(∗) level of theory in aqueous phase with polarizable continuum solvation model (PCM) for the methylation of phosphonate ester monoanion of the soman-aged adduct. The calculated free energy of activation for the methyl transfer process from designed dimethyl(phenyl)sulfonium (1) to aged AChE-OP adduct occurs with a barrier of 31.4kcal/mol at M05-2X/6-31G(∗) level of theory, which is 6.4kcal/mol lower compared to the aging process signifies the preferential reversal process to recover the aged AChE-OP adduct. The pyridine ring containing alkylated sulfonium species, dimethyl(pyridin-2-yl)sulfonium (2), reduced the free energy of activation by 4.4kcal/mol compared to the previously reported alkylating agent N-methyl-2-methoxypyridinium species (A) for the alkylation of aged AChE-OP adduct. The free enzyme can be liberated from the inhibited acetylcholinesterase with the sulfonium compound decorated with an oxime group to avoid the administration of oxime drugs separately. The calculated potential energy surfaces show that the oxime based sulfonium compound (3) can effectively methylate the aged phosphonate ester monoanion of soman aged-adduct. The calculated global reactivity descriptors of the oxime 3 also shed light on this observation. To gain better understanding for protein drug interaction as well as the unbinding and conformational changes of the drug candidate in the active site of cholinesterase, steered molecular dynamics (SMD) simulation with 3 has been performed. Through a protein-drug interaction parameters (rupture force profiles, hydrogen bonds, hydrophobic interactions), geometrical and the orientation of drug-like candidate, the oxime 3 suggests to orchestrate the better reactivation process. The docking studies have been performed with 3 in the aged AChE and BChE to obtain the initial geometry of the SMD studies. The docking methods adopted in this study have been verified with the available crystal geometry of 1-methyl-2-(pentafluorobenzyloxyimino)pyridinium compound in aged soman inhibited human BChE (PDB code: 4B0P). The computational study suggests that the newly designed oxime is a potential candidate to reactivate the aged-AChE adduct.
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