Article
Crystallography
Stephanie Luedtke, Celine Bojo, Yunshen Li, Emilio Luna, Bianca Pomar, Zoran Radic
Summary: The structures of OP-inhibited human acetylcholinesterases have shown similar backbone conformations except for the diethylphosphoryl-hAChE conjugate, where large ethoxy group insertion led to notable loop distortions. Despite the snug fit of large substituents on phosphorus, only minor conformational changes were detected in Novichok-conjugated hAChEs due to the movement of the entire OP away from the acyl pocket. The observation that AChE's small acyl pocket can accommodate larger substituents if the OP is pulled away has practical implications for structure-based design and specificity definition.
Article
Crystallography
Zoran Radic
Summary: The study analyzed the influence of ligand binding on the backbone structures of human, mouse, and Torpedo californica acetylcholinesterase, revealing that the acyl pocket loop is the most conformationally adaptive element. Ligand binding can trigger potential allosteric interactions within the AChE backbone, while the aromatic choline binding site has a stabilizing effect by attracting and pulling fitting entities covalently tethered to the active Ser, facilitating catalytic reactions or relieving steric pressure. These dynamic properties inferred from static X-ray structures contribute to a better understanding of the molecular template important for designing therapeutically active molecules like AChE inhibitors and reactivators of conjugated, inactive AChE.
Article
Biochemistry & Molecular Biology
Hyun Myung Lee, Rudolf Andrys, Jakub Jonczyk, Kyuneun Kim, Avinash G. Vishakantegowda, David Malinak, Adam Skarka, Monika Schmidt, Michaela Vaskova, Kamil Latka, Marek Bajda, Young-Sik Jung, Barbara Malawska, Kamil Musilek
Summary: The designed and synthesised pyridinium-2-carbaldoximes with quinolinium carboxamide moiety showed intermediate-to-high inhibition of both cholinesterases compared to standard oximes. In vitro evaluation revealed their reactivation ability on human recombinant acetylcholinesterase (hrAChE) and human recombinant butyrylcholinesterase (hrBChE), with one compound showing reactivation of all used organophosphates on hrAChE, and two novel compounds able to reactivate NIMP/NEMP-hrBChE. The molecular modelling results highlighted the importance of creating a pre-reactivation complex for better reactivation of both cholinesterases.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2021)
Article
Food Science & Technology
Jana Zdarova Karasova, Jiri Kassa, Vendula Hepnarova, Jaroslav Pejchal, Lucie Junova, Rudolf Andrys, David Malinak, Petr Bzonek, Zuzana Kohoutova, Kamil Musilek
Summary: This study reports the toxicity, pharmacokinetics, and reactivation effectiveness of o-chlorinated bispyridinium oxime K870. K870 showed a safe profile at a dose of 30 mg/kg in rats and exhibited rapid absorption and renal clearance. It efficiently reactivated blood acetylcholinesterase in rats and protected against intoxication by all tested organophosphates in mice.
FOOD AND CHEMICAL TOXICOLOGY
(2022)
Article
Chemistry, Medicinal
Tamara Zorbaz, David Malinak, Tereza Hofmanova, Nikola Marakovic, Suzana Zunec, Nikolina Macek Hrvat, Rudolf Andrys, Miroslav Psotka, Antonio Zandona, Jana Svobodova, Lukas Prchal, Sanja Fingler, Maja Katalinic, Zrinka Kovarik, Kamil Musilek
Summary: Fluorinated bis-pyridinium oximes were designed and synthesized to increase their nucleophilicity and reactivation potential. Compared to non-halogenated oximes, halogenated oximes showed higher binding affinity and lower pKa values. Molecular modeling confirmed the advantage of halogen substitution in stabilizing the oxime and enhancing nucleophilic attack. In vivo administration of a highly efficient reactivator demonstrated significant protection against sarin and cyclosarin exposure.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Goran Sinko
Summary: Currently, only four antidotes are available for treating poisoning by organophosphorus compounds. Many newly designed compounds fail at the enzyme level due to unfavorable interactions within the active site, hindering successful reactivation. Modeling a phosphorylated oxime (POX) can help understand the role of active site residues in the formation of a Michaelis-type complex. Molecular dynamics was used to test the stability of the oxime near the phosphorylated serine in order to study interactions between the AChE oxyanion hole and the phosphorylated oxime.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Article
Pharmacology & Pharmacy
Royce H. Nichols, Janice E. Chambers
Summary: Organophosphorus compounds, including nerve agents and insecticides, inhibit acetylcholinesterase in the nervous system, leading to severe symptoms. The current oximes used in therapy have limitations, but reactivation of serum butyrylcholinesterase may provide an alternative strategy to enhance therapeutic efficacy.
Article
Pharmacology & Pharmacy
Darya A. Kuznetsova, Gulnara A. Gaynanova, Elmira A. Vasilieva, Rais Pavlov, Irina Zueva, Vasily M. Babaev, Denis M. Kuznetsov, Alexandra D. Voloshina, Konstantin A. Petrov, Lucia Y. Zakharova, Oleg G. Sinyashin
Summary: Modified liposomes were developed to deliver the AChE reactivator into the brain, overcoming the low ability of existing antidotes to cross the blood-brain barrier. Results showed that these modified liposomes can reactivate brain AChE and reduce neuronal death caused by poisoning.
Article
Chemistry, Medicinal
Zhao Wei, Jie Yang, Yanqin Liu, Huifang Nie, Lin Yao, Jun Yang, Lei Guo, Zhibing Zheng, Qin Ouyang
Summary: Covalent drugs are important in anti-tumor and antiviral fields, but may have serious toxic effects. Reactivation process of organophosphate-inhibited acetylcholinesterase is not fully understood. Newly optimized compounds based on molecular dynamics simulations were proven to be more efficient reactivators.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Mary E. Dail, Meghan L. M. Brino, Janice E. Chambers
Summary: This study demonstrates that novel oxime compounds can better penetrate the blood-brain barrier, reduce brain damage caused by nerve agents, and provide improved protection.
JOURNAL OF BIOCHEMICAL AND MOLECULAR TOXICOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Hannah. A. A. Minas, Romain M. M. Francois, Franziska Hemmerling, Amy. E. E. Fraley, Cora. L. L. Dieterich, Simon. H. H. Ruedisser, Roy. A. A. Meoded, Sabrina Collin, Kira. J. J. Weissman, Arnaud Gruez, Jorn Piel
Summary: Modular trans-acyltransferase polyketide synthases (trans-AT PKSs) are enzymatic assembly lines that introduce remarkable chemical diversity into their polyketide products. This study focuses on the lobatamide A PKS, which incorporates a methylated oxime. By analyzing the structure and mutagenesis of the oxygenase, the authors propose a catalysis model and identify key protein-protein interactions. This work expands the biomolecular toolbox for trans-AT PKS engineering and enables the introduction of masked aldehyde functionalities into diverse polyketides.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Marina M. Shulaeva, Irina V. Zueva, Anton E. Nikolaev, Liliya F. Saifina, Dilyara R. Sharafutdinova, Vasily M. Babaev, Vyacheslav E. Semenov, Konstantin A. Petrov
Summary: This study synthesized a series of new compounds and verified their effectiveness as reactivators of cholinesterase in the presence of organophosphate inhibitors through in vitro and in vivo experiments. The lead compound, 3e, demonstrated excellent reactivation ability not only in rat brain tissues but also in reducing neurodegeneration and preventing memory impairment.
BIOORGANIC CHEMISTRY
(2023)
Article
Medicine, Research & Experimental
Rudolf Andrys, Aneta Klusonova, Miroslav Lisa, Jiri Kassa, Jana Zd'arova Karasova
Summary: Oxime-based molecules are used to reactivate AChE function in patients with organophosphate intoxication, but their efficacy is limited by low brain penetration. In this study, the use of cucurbit[7]uril (CB[7]) as a carrier for the clinical agent asoxime significantly enhanced its bioavailability in the brain. Pharmacokinetic analysis showed over a 3-fold increase in brain activity when asoxime was administered as a complex with CB[7] compared to alone.
MOLECULAR PHARMACEUTICS
(2021)
Article
Chemistry, Medicinal
Ashima Thakur, Jayant Patwa, Abha Sharma, Swaran Jeet Singh Flora
Summary: The study aimed to synthesize and evaluate a heterocyclic oxime as a reactivator against paraoxon inhibited acetylcholinesterase. The results showed that the synthesized molecules met the criteria for a successful CNS drug candidate and had reasonable reactivation potential against paraoxon-inhibited AChE. Further research is needed to design more efficient uncharged reactivators based on this scaffold.
MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Dongjae Lee, Jieun Choi, Min June Yang, Chin-Ju Park, Jiwon Seo
Summary: This study investigates the influence of structural changes on chameleonic behavior and membrane permeability of the cyclosporin O (CsO) scaffold by controlling backbone and side chain modifications. The results show that beta-hydroxylation at specific positions enhances permeability, while the introduction of additional transannular H-bond slows down the permeation rate. These findings contribute to the discovery of potent macrocycles capable of targeting undruggable targets.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Donald K. Blumenthal, Xiaolin Cheng, Mikolai Fajer, Kwok-Yiu Ho, Jacqueline Rohrer, Oksana Gerlits, Palmer Taylor, Puneet Juneja, Andrey Kovalevsky, Zoran Radic
Summary: The study reveals that homodimerization of acetylcholinesterase can be influenced by factors like phosphorylation at the active site, which can be reversed by structurally diverse oximes. The inability of homodimer dissociation in the case of structural changes in the active site suggests its crucial role in allosterically triggered dissociation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Xiaotian Kong, Enming Xing, Tony Zhuang, Pui-Kai Li, Xiaolin Cheng
Summary: Through an integrated computational study, it was found that BF3 inhibitors inhibit AR function by allosterically modulating the activation function site (AF2), altering the dynamic coupling with the BF3 and AF2 sites, as well as the AF2-coactivator interaction. The binding energy analyses revealed the anchor role of the linker in these inhibitors and showed differential interactions with specific residues affecting inhibitory activities. Additionally, the allosteric communication pathway analyses demonstrated how signals triggered by BF3 binding are transmitted to the AF2 pocket through multiple transmission pathways.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Yulin Ren, Sijin Wu, Sijie Chen, Joanna E. Burdette, Xiaolin Cheng, A. Douglas Kinghorn
Summary: The study found that (+)-strebloside may be more promising than digoxin in developing potential anticancer agents, as it can target multiple molecular targets and mediate the antitumor activity of cardiac glycosides.
Article
Chemistry, Physical
Daniel W. Kneller, Oksana Gerlits, Luke L. Daemen, Anna Pavlova, James C. Gumbart, Yongqiang Cheng, Andrey Kovalevsky
Summary: Biomacromolecules, such as proteins, exhibit dynamic behavior that is essential for their function. In this study, we investigated the vibrational dynamics of HIV-1 protease upon binding of the antiviral drug darunavir. Our results showed that darunavir caused softening of the protein's vibrational dynamics, with asymmetric effects on different structural elements. Specifically, three secondary structure elements were found to contribute significantly to the changes in vibrational dynamics. Molecular dynamics simulations estimated that the altered dynamics would contribute to the free energy of darunavir binding. These findings provide insights into the relationship between protein dynamics and drug resistance.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Victoria N. Drago, Juliette M. Devos, Matthew P. Blakeley, V. Trevor Forsyth, Andrey Y. Kovalevsky, Constance A. Schall, Timothy C. Mueser
Summary: This article presents a method for growing neutron diffraction-quality crystals of PLP-dependent enzymes using microgravity, aiming to improve the understanding of reaction diversity of these enzymes at an atomic level.
Article
Instruments & Instrumentation
Gloria E. O. Borgstahl, William B. O'Dell, Martin Egli, Jan F. Kern, Andrey Kovalevsky, Jiao Y. Y. Lin, Dean Myles, Mark A. Wilson, Wen Zhang, Petrus Zwart, Leighton Coates
Summary: Neutron macromolecular crystallography (NMC) is crucial for revealing the positions of all atoms in large macromolecules due to its sensitive and gentle probing capabilities. The new design of EWALD will overcome the crystal volume barrier and enable new types of experiments, study of grand challenge systems, and more routine use of NMC in biology.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2022)
Article
Engineering, Biomedical
Abhjeet S. Bhullar, Long Zhang, Nicolas Burns, Xiaolin Cheng, Peixuan Guo
Summary: Researchers have discovered and constructed a durable nanoscale bio-aperture that can regulate current at the pico-ampere scale. The aperture is made of 12 identical protein subunits and has a shutter and one-way traffic property. This discovery has important implications for nanodevices and disease diagnosis.
Article
Chemistry, Physical
Zoe Li, Kevin C. Chan, Jonathan D. Nickels, Xiaolin Cheng
Summary: Biomolecular binding relies on specific attractive interactions between partner molecules. This study examines the electrostatic contributions to nicotine binding by simulating the binding free energy of nicotine and acetylcholine binding protein (AChBP). The simulations reveal that nicotine binds AChBP predominantly in its charged form, and the binding is driven by electrostatic interactions, cation-pi interactions, and hydrogen bonding. Van der Waals interactions also play a role in the binding process.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biology
Nashaat T. Nashed, Daniel W. Kneller, Leighton Coates, Rodolfo Ghirlando, Annie Aniana, Andrey Kovalevsky, John M. Louis
Summary: This study investigates the structural characterization and catalytic activity of SARS-Cov-2 main protease, revealing that inhibitor-induced conformational changes of the oxyanion loop are key to dimer formation. Mass spectrometry and crystal structure analysis demonstrate the modulatory role of structural changes in autoprocessing of the main protease.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Medicinal
Zoe Li, Kevin C. Chan, Jonathan D. Nickels, Xiaolin Cheng
Summary: Pentameric ligand-gated ion channels, including 5-HT3 receptors, are important for fast neurotransmissions and clinical treatment of chemotherapy-induced nausea and vomiting. This study presents a refined equilibration protocol to stabilize open state structures of the 5-HT3 receptor, allowing water and ion permeation through the channel. The findings highlight the conformational coupling between transmembrane helices as crucial for achieving stable open-like structures.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Plant Sciences
Yulin Ren, Elizabeth N. Kaweesa, Lei Tian, Sijin Wu, Kongmany Sydara, Mouachanh Xayvue, Curtis E. Moore, Djaja D. Soejarto, Xiaolin Cheng, Jianhua Yu, Joanna E. Burdette, A. Douglas Kinghorn
Summary: A cardiac glycoside epoxide, (-)-cryptanoside A (1), was isolated from Cryptolepis dubia and showed potent cytotoxicity against various human cancer cell lines. It also inhibited Na+/K+-ATPase activity and increased the expression of Akt and the p65 subunit of NF-κB. Molecular docking analysis suggested that (-)-cryptanoside A (1) directly targets Na(+)/K+-ATPase to exhibit its cytotoxic effects on cancer cells.
JOURNAL OF NATURAL PRODUCTS
(2023)
Article
Chemistry, Multidisciplinary
Bo Sun, Xingchu Zhao, Birui Xu, Erzheng Su, Andrey Kovalevsky, Qirong Shen, Dongyang Liu, Qun Wan
Summary: In this study, a hyperthermophilic chitinase (ActChi) was discovered, which can directly hydrolyze crystalline chitin at its optimal temperature of 80°C. By introducing a heterogeneous and hyperthermophilic chitin binding domain (ChBD) at the N-terminus of CDchi, the activity and thermostability of the enzyme were significantly enhanced. This strategy provides a good example of green sustainable degradation for crystalline biopolymers in nature.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Victoria N. N. Drago, Claudia Campos, Mattea Hooper, Aliyah Collins, Oksana Gerlits, Kevin L. L. Weiss, Matthew P. P. Blakeley, Robert S. S. Phillips, Andrey Kovalevsky
Summary: The authors determined the structure of Thermus thermophilus SHMT using X-ray/neutron crystallography and proposed its catalytic mechanism. This is important for drug design and enzyme engineering.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Victoria N. Drago, Steven Dajnowicz, Jerry M. Parks, Matthew P. Blakeley, David A. Keen, Nicolas Coquelle, Kevin L. Weiss, Oksana Gerlits, Andrey Kovalevsky, Timothy C. Mueser
Summary: The study focuses on the role of pyridoxal 5'-phosphate (PLP)-dependent enzyme in promoting various chemical reactions and the use of neutron crystallography to visualize the electron states of PLP and enzyme active sites. The researchers report a joint X-ray/neutron structure of aspartate aminotransferase (AAT) with pyridoxamine 5'-phosphate (PMP), providing evidence of a low-barrier hydrogen bond (LBHB) interaction. The findings suggest that the LBHB facilitates the preorganization of the active site for the subsequent reaction.
Article
Chemistry, Physical
Zhenyu Wang, Wanying Huang, Manjun Liu, Stephen J. Kennel, Jonathan S. Wall, Xiaolin Cheng
Summary: The study focused on the dynamic interactions between a newly synthesized peptide P62 and a structural model of lambda light chain in systemic amyloidosis. It was found that P62 binds only to the canonical interface of the fibril and the lysine residues of P62 play an important role in the binding process by forming initial contacts with aspartic acids on the fibril surface.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)