51
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Hei B, Tardiff JC, Schwartz SD. Human cardiac β-myosin powerstroke energetics: Thin filament, Pi displacement, and mutation effects. Biophys J 2024; 123:3133-3142. [PMID: 39001604 PMCID: PMC11427785 DOI: 10.1016/j.bpj.2024.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/01/2024] [Accepted: 07/09/2024] [Indexed: 07/25/2024] Open
Abstract
The powerstroke of human cardiac β-myosin is an important stage of the cross-bridge cycle that generates force for muscle contraction. However, the starting structure of this process has never been resolved, and the relative timing of the powerstroke and inorganic phosphate (Pi) release is still controversial. In this study, we generated an atomistic model of myosin on the thin filament and utilized metadynamics simulations to predict the absent starting structure of the powerstroke. We demonstrated that the displacement of Pi from the active site during the powerstroke is likely necessary, reducing the energy barrier of the conformation change. The effects of the presence of the thin filament, the hypertrophic cardiomyopathy mutation R712L, and the binding of mavacamten on the powerstroke process were also investigated.
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Affiliation(s)
- Bai Hei
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona
| | - Jil C Tardiff
- Department of Biomedical Engineering, University of Arizona, Tucson, Arizona
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona.
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52
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Barragan-Galvez JC, Gonzalez-Rivera ML, Jiménez-Cruz JC, Hernandez-Flores A, de la Rosa G, Lopez-Moreno ML, Yañez-Barrientos E, Romero-Hernández M, Deveze-Alvarez MA, Navarro-Santos P, Acosta-Mata C, Isiordia-Espinoza MA, Alonso-Castro AJ. A Patent-Pending Ointment Containing Extracts of Five Different Plants Showed Antinociceptive and Anti-Inflammatory Mechanisms in Preclinical Studies. Pharmaceutics 2024; 16:1215. [PMID: 39339251 PMCID: PMC11435228 DOI: 10.3390/pharmaceutics16091215] [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: 07/11/2024] [Revised: 09/10/2024] [Accepted: 09/11/2024] [Indexed: 09/30/2024] Open
Abstract
Background/Objectives: The antinociceptive and anti-inflammatory effects of a patent-pending ointment containing plant extracts from Eucalyptus globulus, Curcuma longa, Hamamelis virginiana, Echinacea purpurea, and Zingiber officinale were evaluated. Methods: Plant extracts were chemically characterized by gas chromatography-mass spectroscopy. The antinociceptive activity of the ointment was assessed using the hot plate, tail flick, and formalin tests, whereas the anti-inflammatory activity was measured using the acute and chronic TPA-induced ear edema tests. Mechanisms of action were evaluated using inhibitors from signaling pathways related to pain response and by using histological analysis and assessing the expression and activity of pro-inflammatory mediators. Results: The ointment showed antinociceptive and anti-inflammatory effects like those observed with diclofenac gel (1.16% v/v) and ketoprofen gel (2.5% v/v). The antinociceptive actions of the ointment are mediated by the possible participation of the opiodergic system and the nitric oxide pathway. The anti-inflammatory response was characterized by a decrease in myeloperoxidase (MPO) activity and by a reduction in ear swelling and monocyte infiltration in the acute inflammation model. In the chronic model, the mechanism of action relied on a decrease in pro-inflammatory mediators such as COX-2, IL-1β, TNF-α, and MPO. An in-silico study with myristic acid, one of the compounds identified in the ointment's plant mixture, corroborated the in vivo results. Conclusions: The ointment showed antinociceptive activities mediated by the decrease in COX-2 and NO levels, and anti-inflammatory activity due to the reduction in IL-1β and TNFα levels, a reduction in MPO activity, and a decrease in NF-κB and COX-2 expression.
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Affiliation(s)
- Juan Carlos Barragan-Galvez
- Departamento de Farmacia, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36200, Mexico
| | - Maria Leonor Gonzalez-Rivera
- Departamento de Farmacia, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36200, Mexico
| | - Juan C Jiménez-Cruz
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCyT)-Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolas de Hidalgo, Morelia 58030, Mexico
| | - Araceli Hernandez-Flores
- Departamento de Farmacia, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36200, Mexico
- Instituto de Investigación Sobre la Salud Pública, Universidad de la Sierra Sur, Miahuatlán de Porfirio Díaz, Oaxaca 70800, Mexico
| | - Guadalupe de la Rosa
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Campus León, León 37150, Mexico
| | - Martha L Lopez-Moreno
- Chemistry Department, University of Puerto Rico at Mayagüez, 259 Boulevard Alfonso Valdez, Mayagüez 00681, Puerto Rico
| | - Eunice Yañez-Barrientos
- Departamento de Química, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36200, Mexico
| | - Michelle Romero-Hernández
- Departamento de Química, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36200, Mexico
| | - Martha Alicia Deveze-Alvarez
- Departamento de Farmacia, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36200, Mexico
| | - Pedro Navarro-Santos
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCyT)-Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolas de Hidalgo, Morelia 58030, Mexico
| | - Claudia Acosta-Mata
- Laboratorio de Patología Clínica, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Guanajuato 36000, Mexico
| | | | - Angel Josabad Alonso-Castro
- Departamento de Farmacia, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato 36200, Mexico
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53
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McCahill AL, Zhang T, Saven JG, Kloxin CJ, Pochan DJ. Peptide Bundlemer Networks or Lattices: Controlling Cross-Linking and Self-Assembly Using Protein-like Display of Chemistry. ACS NANO 2024; 18:25695-25707. [PMID: 39228265 DOI: 10.1021/acsnano.4c07961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Coiled-coil 'bundlemer' peptides were selectively modified with allyloxycarbonyl (alloc)-protected lysine, a non-natural amino acid containing an alkene on its side chain. The specific display of this alkene from the coiled-coil surface with protein-like specificity enabled this residue to be used as a covalent linkage for creating peptide networks with controllable properties or as a physical linkage for the self-assembly of bundlemers into unexpected, intricate lattices driven by the hydrophobic nature of the side chain. For network formation, peptides were modified with both alloc-protected lysine and cysteine amino acids for solution assembly into solvent-swollen films and subsequent covalent cross-linking via thiol-ene photo click reactions. The degree of network cross-linking, as determined by rheometry, was finely tuned by varying the specific spatial display of reactive groups on the bundlemer building block particles, transitioning between intrabundle and interbundle cross-linking. The designed display of alloc groups from the center of the bundlemer building block also prompted particle self-assembly into an unexpected intricate lattice with a porous morphology. The lattices were studied in a variety of solution conditions using transmission electron microscopy, cryotransmission electron microscopy, and small-angle X-ray scattering. The approximate particle arrangement in the lattice was determined by using coarse-grained modeling and machine learning optimization techniques along with experimental methods. The proposed truss-like face-centered cubic packing of the alloc-functionalized bundlemers agrees well with the experimental results.
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Affiliation(s)
- Amanda L McCahill
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Tianren Zhang
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
- Department of Chemistry, University of Pennsylvania, Philadelphia, Philadelphia 19104, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Philadelphia 19104, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
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54
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Chen X, Wang K, Chen J, Wu C, Mao J, Song Y, Liu Y, Shao Z, Pu X. Integrative residue-intuitive machine learning and MD Approach to Unveil Allosteric Site and Mechanism for β2AR. Nat Commun 2024; 15:8130. [PMID: 39285201 PMCID: PMC11405859 DOI: 10.1038/s41467-024-52399-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 09/03/2024] [Indexed: 09/20/2024] Open
Abstract
Allosteric drugs offer a new avenue for modern drug design. However, the identification of cryptic allosteric sites presents a formidable challenge. Following the allostery nature of residue-driven conformation transition, we propose a state-of-the-art computational pipeline by developing a residue-intuitive hybrid machine learning (RHML) model coupled with molecular dynamics (MD) simulation, through which we can efficiently identify the allosteric site and allosteric modulator as well as reveal their regulation mechanism. For the clinical target β2-adrenoceptor (β2AR), we discover an additional allosteric site located around residues D792.50, F2826.44, N3187.45 and S3197.46 and one putative allosteric modulator ZINC5042. Using Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and protein structure network (PSN), the allosteric potency and regulation mechanism are probed to further improve identification accuracy. Benefiting from sufficient computational evidence, the experimental assays then validate our predicted allosteric site, negative allosteric potency and regulation pathway, showcasing the effectiveness of the identification pipeline in practice. We expect that it will be applicable to other target proteins.
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Affiliation(s)
- Xin Chen
- College of Chemistry, Sichuan University, Chengdu, China
| | - Kexin Wang
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Jianfang Chen
- College of Chemistry, Sichuan University, Chengdu, China
| | - Chao Wu
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Mao
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yuanpeng Song
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yijing Liu
- College of Computer Science, Sichuan University, Chengdu, China
| | - Zhenhua Shao
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, China.
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu, China.
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55
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Hu KQ, Luo XJ, Zeng YH, Liu Y, Mai BX. Species-specific metabolism of triphenyl phosphate and its mono-hydroxylated product by human and rat CYP2E1 and the carp ortholog. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116748. [PMID: 39059342 DOI: 10.1016/j.ecoenv.2024.116748] [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: 01/23/2024] [Revised: 06/13/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
Organophosphorus flame retardants (PFRs) are a class of flame retardants and environmental pollutants with various biological effects. Recentstudies have evidenced activation of some PFRs by human CYP enzymes (including CYP2E1) for genotoxic effects. However, the activity of CYPs in fish species toward PFR metabolism remains unclear. This study was aimed on comparing the metabolism of triphenyl phosphate (TPHP) and 4-OH-TPHP in human, rat, and common carp, and the involvement of human CYP2E1 and its orthologs in the metabolism, by using fomepizole (4-MP, CYP2E1 inhibitor) as a modulator, in silico molecular docking and dynamics analyses. The rate of TPHP metabolism was apparently faster with human and rat, microsomes than with fish microsomes, the major metabolites were phosphodiester and hydroxylated phosphate, with 30-80 % of TPHP forming unidentified metabolites in the system of each species. 4-OH-TPHP was readily metabolized by both human and rat microsomes, whereas it was hardly metabolized in carp assays. Meanwhile, with 4-MP the transformation of TPHP to 4-OH-TPHP was enhanced in the human/rat systems while suppressed in the carp system. Moreover, the formation of unidentified metabolites in human and rat systems was mostly inhibited by 4-MP. Through molecular dynamics analysis TPHP and its primary metabolites showed high affinity for human and rat CYP2E1, as well as the carp ortholog (CYP2G1-like enzyme), however, the 4-OH-TPHP bond to the latter was too far from the heme to permit a biochemical reaction. This study suggests that the metabolism/activation of TPHP might be favored in mammals rather than carp, a fish species.
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Affiliation(s)
- Ke-Qi Hu
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Resources Utilization and Protection, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Xiao-Jun Luo
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Resources Utilization and Protection, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China.
| | - Yan-Hong Zeng
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Resources Utilization and Protection, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| | - Yungang Liu
- Department of Toxicology, School of Public Health (Guangdong Provincial Key Laboratory of Tropical Disease Research), Southern Medical University, 1023 S. Shatai Road, Guangzhou 510515, China
| | - Bi-Xian Mai
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Resources Utilization and Protection, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
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56
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Abdulla A, Abudureheman T, Chen K, Ghalandari B, Yan H, Zhou H, Su H, Zhang Y, Duan CW, Ding X. Efficient Capture and Traceless Release of Functional CD8 + T Cells with a Microfluidic Chip for Enhanced In Vitro and In Vivo CD4-CAR Transduction. Anal Chem 2024. [PMID: 39269432 DOI: 10.1021/acs.analchem.4c03135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
Abstract
The chimeric antigen receptor (CAR) T cells targeting CD4 expressed cells in acute lymphoblastic leukemia (T-ALL) and acute myeloid leukemia (AML) could reduce the risk of off target effects in normal tissues. However, the efficacy of adoptive cell therapy is predominantly attributed to CD8+ T cells, necessitating their purification before lentivirus transfection to enhance the production of CD4-CAR-T cells. In this study, we developed a microfluidic chip functionalized with an optimized CD8 aptamer, A3t-MU, to facilitate the enrichment and purification of CD8+ T cells. The presented chip showed efficient capture and seamless release of CD8+ T cells from cultured T cells and peripheral blood mononuclear cells (PBMCs). The purity of the released CD8+ T cells reached 98.1%, representing a 13% improvement over the conventional magnetic bead separation method. CD4-CAR was efficiently transduced into the purified CD8+ T cells to construct CAR-T cells. We evaluated the antitumor capability of the CD4-CAR transduced CD8+ T cells (anti-CD4 CD8-CAR T cells) both in vitro and in vivo. The anti-CD4 CD8-CAR T cells exhibited significant cancer-cell-killing capacity across multiple tumor cell lines, including CEM, Jurkat, and MV4-11. Meanwhile, anti-CD4 CD8-CAR T cells significantly inhibited tumor growth in vivo. In conclusion, the presented microfluidic chip offers a cost-effective and high-purity approach for CD8+ T cell separation, enhancing CD4-CAR transduction and achieving efficient antitumor capability both in vitro and in vivo.
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Affiliation(s)
- Aynur Abdulla
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200092, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Tuersunayi Abudureheman
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Kaiming Chen
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Behafarid Ghalandari
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Haoni Yan
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Hang Zhou
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Hengxing Su
- Department of Neurosurgery, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, China
| | - Yunqian Zhang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Cai-Wen Duan
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Pediatric Translational Medicine Institute Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Xianting Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200092, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
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57
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Daly CA, Seebald LM, Wolk E. Employing Metadynamics to Predict the Membrane Partitioning of Carboxy-2 H-Azirine Natural Products. J Phys Chem B 2024; 128:8771-8781. [PMID: 39225398 PMCID: PMC11403667 DOI: 10.1021/acs.jpcb.4c03411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Natural products containing the carboxy-2H-azirine moiety are an exciting target for investigation due to their broad-spectrum antimicrobial activity and new chemical space they afford for novel therapeutic development. The carboxy-2H-azirine moiety, including those appended to well-characterized chemical scaffolds, is understudied, which creates a challenge for understanding potential modes of inhibition. In particular, some known natural product carboxy-2H-azirines have long hydrophobic tails, which could implicate them in membrane-associated processes. In this study, we examined a small set of carboxy-2H-azirine natural products with varied structural features that could alter membrane partitioning. We compared the predicted membrane partitioning and alignment of these compounds to those of established membrane embedders with similar chemical scaffolds. To accomplish this, we developed parameters within the framework of the CHARMM36 force field for the 2H-azirine functional group and performed metadynamics simulations of the partitioning into a model bacterial membrane from aqueous solution. We determined that the carboxy-2H-azirine functional group is strongly hydrophilic, imbuing the long-chain natural products with amphipathicity similar to the known membrane-embedding molecules to which they were compared. For the long-chain analogs, the carboxy-2H-azirine head group stays within 1 nm of the phosphate layer, while the hydrophobic tail sits within the membrane. The carboxy-2H-azirine lacking the long alkyl chain instead partitions completely into aqueous solution.
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Affiliation(s)
- Clyde A Daly
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, United States
| | - Leah M Seebald
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, United States
| | - Emma Wolk
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, United States
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58
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Bodosa J, Klauda JB. Metadynamics Study of Lipid-Mediated Antibacterial Toxin Binding to the EmrE Multiefflux Protein. J Phys Chem B 2024; 128:8712-8723. [PMID: 39197021 DOI: 10.1021/acs.jpcb.4c02807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2024]
Abstract
EmrE is a bacterial efflux protein in the small multidrug-resistant (SMR) family present in Escherichia coli. Due to its small size, 110 residues in each dimer subunit, it is an ideal model system to study ligand-protein-membrane interactions. Here in our work, we have calculated the free energy landscape of benzyltrimetylammonium (BTMA) and tetraphenyl phosphonium (TPP) binding to EmrE using the enhanced sampling method-multiple walker metadynamics. We estimate that the free energy of BTMA binding to EmrE is -21.2 ± 3.3 kJ/mol and for TPP is -43.6 ± 3.8 kJ/mol. BTMA passes through two metastable states to reach the binding pocket, while TPP has a more complex binding landscape with four metastable states and one main binding site. Our simulations show that the ligands interact with the membrane lipids at a distance 1 nm away from the binding site which forms a broad local minimum, consistent for both BTMA and TPP. This site can be an alternate entry point for ligands to partition from the membrane into the protein, especially for bulky and/or branched ligands. We also observed the membrane lipid and C-terminal 110HisA form salt-bridge interactions with the helix-1 residue 22LysB. Our free energy estimates and clusters are in close agreement with experimental data and give us an atomistic view of the ligand-protein-lipid interactions. Understanding the binding pathway of these ligands can guide us in future design of ligands that can alter or halt the function of EmrE.
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Affiliation(s)
- Jessica Bodosa
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Jeffery B Klauda
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
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59
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Luo X, Seidler M, Lee YJ, Yu T, Zuckermann RN, Balsara NP, Abel BA, Prendergast D, Jiang X. Evaluating Cryo-TEM Reconstruction Accuracy of Self-Assembled Polymer Nanostructures. Macromol Rapid Commun 2024:e2400589. [PMID: 39264522 DOI: 10.1002/marc.202400589] [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: 07/18/2024] [Revised: 08/30/2024] [Indexed: 09/13/2024]
Abstract
Cryogenic transmission electron microscopy (cryo-TEM) combined with single particle analysis (SPA) is an emerging imaging approach for soft materials. However, the accuracy of SPA-reconstructed nanostructures, particularly those formed by synthetic polymers, remains uncertain due to potential packing heterogeneity of the nanostructures. In this study, the combination of molecular dynamics (MD) simulations and image simulations is utilized to validate the accuracy of cryo-TEM 3D reconstructions of self-assembled polypeptoid fibril nanostructures. Using CryoSPARC software, image simulations, 2D classifications, ab initio reconstructions, and homogenous refinements are performed. By comparing the results with atomic models, the recovery of molecular details is assessed, heterogeneous structures are identified, and the influence of extraction location on the reconstructions is evaluated. These findings confirm the fidelity of single particle analysis in accurately resolving complex structural characteristics and heterogeneous structures, exhibiting its potential as a valuable tool for detailed structural analysis of synthetic polymers and soft materials.
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Affiliation(s)
- Xubo Luo
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Morgan Seidler
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Yen Jea Lee
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Tianyi Yu
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ronald N Zuckermann
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nitash P Balsara
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Brooks A Abel
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - David Prendergast
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xi Jiang
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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60
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Barrett SE, Yin S, Jordan P, Brunson JK, Gordon-Nunez J, Costa Machado da Cruz G, Rosario C, Okada BK, Anderson K, Pires TA, Wang R, Shukla D, Burk MJ, Mitchell DA. Substrate interactions guide cyclase engineering and lasso peptide diversification. Nat Chem Biol 2024:10.1038/s41589-024-01727-w. [PMID: 39261643 DOI: 10.1038/s41589-024-01727-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 08/12/2024] [Indexed: 09/13/2024]
Abstract
Lasso peptides are a diverse class of naturally occurring, highly stable molecules kinetically trapped in a distinctive [1]rotaxane conformation. How the ATP-dependent lasso cyclase constrains a relatively unstructured substrate peptide into a low entropy product has remained a mystery owing to poor enzyme stability and activity in vitro. In this study, we combined substrate tolerance data with structural predictions, bioinformatic analysis, molecular dynamics simulations and mutational scanning to construct a model for the three-dimensional orientation of the substrate peptide in the lasso cyclase active site. Predicted peptide cyclase molecular contacts were validated by rationally engineering multiple, phylogenetically diverse lasso cyclases to accept substrates rejected by the wild-type enzymes. Finally, we demonstrate the utility of lasso cyclase engineering by robustly producing previously inaccessible variants that tightly bind to integrin αvβ8, which is a primary activator of transforming growth factor β and, thus, an important anti-cancer target.
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Affiliation(s)
- Susanna E Barrett
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Song Yin
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | | | | | | | | | | | | | | | - Thomas A Pires
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Ruoyang Wang
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Diwakar Shukla
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | | | - Douglas A Mitchell
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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Xu M, Zhao Z, Deng P, Sun M, Chiu CKC, Wu Y, Wang H, Bi Y. Functional Divergence in the Affinity and Stability of Non-Canonical Cysteines and Non-Canonical Disulfide Bonds: Insights from a VHH and VNAR Study. Int J Mol Sci 2024; 25:9801. [PMID: 39337289 PMCID: PMC11432006 DOI: 10.3390/ijms25189801] [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: 08/01/2024] [Revised: 09/03/2024] [Accepted: 09/05/2024] [Indexed: 09/30/2024] Open
Abstract
Single-domain antibodies, including variable domains of the heavy chains of heavy chain-only antibodies (VHHs) from camelids and variable domains of immunoglobulin new antigen receptors (VNARs) from cartilaginous fish, show the therapeutic potential of targeting antigens in a cytosol reducing environment. A large proportion of single-domain antibodies contain non-canonical cysteines and corresponding non-canonical disulfide bonds situated on the protein surface, rendering them vulnerable to environmental factors. Research on non-canonical disulfide bonds has been limited, with a focus solely on VHHs and utilizing only cysteine mutations rather than the reducing agent treatment. In this study, we examined an anti-lysozyme VNAR and an anti-BC2-tag VHH, including their non-canonical disulfide bond reduced counterparts and non-canonical cysteine mutants. Both the affinity and stability of the VNARs and VHHs decreased in the non-canonical cysteine mutants, whereas the reduced-state samples exhibited decreased thermal stability, with their affinity remaining almost unchanged regardless of the presence of reducing agents. Molecular dynamics simulations suggested that the decrease in affinity of the mutants resulted from increased flexibility of the CDRs, the disappearance of non-canonical cysteine-antigen interactions, and the perturbation of other antigen-interacting residues caused by mutations. These findings highlight the significance of non-canonical cysteines for the affinity of single-domain antibodies and demonstrate that the mutation of non-canonical cysteines is not equivalent to the disruption of non-canonical disulfide bonds with a reducing agent when assessing the function of non-canonical disulfide bonds.
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Affiliation(s)
- Mingce Xu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Zhao
- School of Data Science, University of Virginia, Charlottesville, VA 22904, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Penghui Deng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengsi Sun
- Shenzhen Bay Laboratory, Shenzhen 518055, China
| | | | - Yujie Wu
- Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Hao Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266071, China
| | - Yunchen Bi
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266071, China
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62
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Del Favero G, Bergen J, Palm L, Fellinger C, Matlaeva M, Szabadi A, Fernandes AS, Saraiva N, Schröder C, Marko D. Short-Term Exposure to Foodborne Xenoestrogens Affects Breast Cancer Cell Morphology and Motility Relevant for Metastatic Behavior In Vitro. Chem Res Toxicol 2024. [PMID: 39262136 DOI: 10.1021/acs.chemrestox.4c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Breast cancer is highly susceptible to metastasis formation. During the time of disease progression, tumor pathophysiology can be impacted by endogenous factors, like hormonal status, as well as by environmental exposures, such as those related to diet and lifestyle. New lines of evidence point toward a potential role for foodborne endocrine disruptive chemicals in this respect; however, mechanistic understanding remains limited. At the molecular level, crucial steps toward metastasis formation include cell structural changes, alteration of adhesion, and reorganization of cytoskeletal proteins involved in motility. Hence, this study investigates the potential of dietary xenoestrogens to impact selected aspects of breast cancer cell mechanotransduction. Taking the onset of the metastatic cascade as a model, experiments focused on cell-matrix adhesion, single-cell migration, and adaptation of cell morphology. Dietary mycoestrogens alternariol (AOH, 1 μM) and α-zearalenol (α-ZEL, 10 nM), soy isoflavone genistein (GEN, 1 μM), and food packaging plasticizer bisphenol A (BPA, 10 nM) were applied as single compounds or in mixtures. Pursuing the hypothesis that endocrine active molecules could affect cell functions beyond the estrogen receptor-dependent cascade, experiments were performed comparing the MCF-7 cell line to the triple negative breast cancer cells MDA MB-231. Indeed, the four compounds functionally affected the motility and the adhesion of both cell types. These responses were coherent with rearrangements of the actin cytoskeleton and with the modulation of the expression of integrin β1 and cathepsin D. Mechanistically, molecular dynamics simulations confirmed a potential interaction with fragments of the α1 and β1 integrin subunits. In sum, dietary xenoestrogens proved effective in modifying the motility and adhesion of breast cancer cells, as predictive end points for metastatic behavior in vitro. These effects were measurable after short incubation times (1 or 8 h) and contribute to shed novel light on the activity of compounds with hormonal mimicry potential in breast cancer progression.
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Affiliation(s)
- Giorgia Del Favero
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Core Facility Multimodal Imaging, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Janice Bergen
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Core Facility Multimodal Imaging, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna 1090, Austria
| | - Lena Palm
- Computational Biological Chemistry Department, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Christian Fellinger
- Computational Biological Chemistry Department, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Vienna 1090, Austria
- Christian Doppler Laboratory for Molecular Informatics in the Biosciences, Department for Pharmaceutical Sciences, University of Vienna, Vienna 1090, Austria
| | - Maria Matlaeva
- Computational Biological Chemistry Department, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - András Szabadi
- Computational Biological Chemistry Department, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Ana Sofia Fernandes
- CBIOS, Universidade Lusófona's Research Center for Biosciences & Health Technologies, Lisboa 1749-024, Portugal
| | - Nuno Saraiva
- CBIOS, Universidade Lusófona's Research Center for Biosciences & Health Technologies, Lisboa 1749-024, Portugal
| | - Christian Schröder
- Computational Biological Chemistry Department, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Doris Marko
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
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63
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Chen Y, Liang D, Lee EMY, Muy S, Guillaume M, Braida MD, Emery AA, Marzari N, de Pablo JJ. Ion Transport at Polymer-Argyrodite Interfaces. ACS APPLIED MATERIALS & INTERFACES 2024; 16:48223-48234. [PMID: 39213640 PMCID: PMC11403566 DOI: 10.1021/acsami.4c07440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Solid-state electrolytes, particularly polymer/ceramic composite electrolytes, are emerging as promising candidates for lithium-ion batteries due to their high ionic conductivity and mechanical flexibility. The interfaces that arise between the inorganic and organic materials in these composites play a crucial role in ion transport mechanisms. While lithium ions are proposed to diffuse across or parallel to the interface, few studies have directly examined the quantitative impact of these pathways on ion transport and little is known about how they affect the overall conductivity. Here, we present an atomistic study of lithium-ion (Li+) transport across well-defined polymer-argyrodite interfaces. We present a force field for polymer-argyrodite interfacial systems, and we carry out molecular dynamics and enhanced sampling simulations of several composite systems, including poly(ethylene oxide) (PEO)/Li6PS5Cl, hydrogenated nitrile butadiene rubber (HNBR)/Li6PS5Cl, and poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP)/Li6PS5Cl. For the materials considered here, Li-ion exhibits a preference for the ceramic material, as revealed by free energy differences for Li-ion between the inorganic and the organic polymer phase in excess of 13 kBT. The relative free energy profiles of Li-ion for different polymeric materials exhibit similar shapes, but their magnitude depends on the strength of interaction between the polymers and Li-ion: the greater the interaction between the polymer and Li-ions, the smaller the free energy difference between the inorganic and organic materials. The influence of the interface is felt over a range of approximately 1.5 nm, after which the behavior of Li-ion in the polymer is comparable to that in the bulk. Near the interface, Li-ion transport primarily occurs parallel to the interfacial plane, and ion mobility is considerably slower near the interface itself, consistent with the reduced segmental mobility of the polymer in the vicinity of the ceramic material. These findings provide insights into ionic complexation and transport mechanisms in composite systems, and will help improve design of improved solid electrolyte systems.
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Affiliation(s)
- Yuxi Chen
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Dongyue Liang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Elizabeth M Y Lee
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, United States
| | - Sokseiha Muy
- Theory and Simulations of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | | | | | | | - Nicola Marzari
- Theory and Simulations of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
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64
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Liu SH, Rukmani SJ, Mohan M, Yu Y, Vural D, Johnson DA, Copenhaver K, Bhagia S, Lamm ME, Li K, Chen J, Goswami M, Smith MD, Petridis L, Ozcan S, Smith JC. Molecular-level design of alternative media for energy-saving pilot-scale fibrillation of nanocellulose. Proc Natl Acad Sci U S A 2024; 121:e2405107121. [PMID: 39236244 PMCID: PMC11406261 DOI: 10.1073/pnas.2405107121] [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: 03/11/2024] [Accepted: 07/23/2024] [Indexed: 09/07/2024] Open
Abstract
The outstanding mechanical properties, light weight, and biodegradability of cellulose nanofibrils (CNFs) make them promising components of renewable and sustainable next-generation reinforced composite biomaterials and bioplastics. Manufacturing CNFs at a pilot scale requires disc-refining fibrillation of dilute cellulose fibers in aqueous pulp suspensions to shear the fibers apart into their nanodimensional forms, which is, however, an energy-intensive process. Here, we used atomistic molecular dynamics (MD) simulation to examine media that might facilitate the reduction of interactions between cellulose fibers, thereby reducing energy consumption in fibrillation. The most suitable medium found by the simulations was an aqueous solution with 0.007:0.012 wt.% NaOH:urea, and indeed this was found in pilot-scale experiments to reduce the fibrillation energy by ~21% on average relative to water alone. The NaOH:urea-mediated CNFs have similar crystallinity, morphology, and mechanical strength to those formed in water. The NaOH and urea act synergistically on CNFs to aid fibrillation but at different length scales. NaOH deprotonates hydroxyl groups leading to mesoscale electrostatic repulsion between fibrils, whereas urea forms hydrogen bonds with protonated hydroxyl groups thus disrupting interfibril hydrogen bonds. This suggests a general mechanism in which an aqueous medium that contains a strong base and a small organic molecule acting as a hydrogen-bond acceptor and/or donor may be effectively employed in materials processes where dispersion of deprotonable polymers is required. The study demonstrates how atomic-detail computer simulation can be integrated with pilot-scale experiments in the rational design of materials processes for the circular bioeconomy.
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Affiliation(s)
- Shih-Hsien Liu
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Shalini J Rukmani
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Mood Mohan
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Yan Yu
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Derya Vural
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
- Department of Physics, Marmara University, Istanbul 34722, Türkiye
| | - Donna A Johnson
- Process Development Center, University of Maine, Orono, ME 04469
| | - Katie Copenhaver
- Manufacturing Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Samarthya Bhagia
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Meghan E Lamm
- Manufacturing Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Kai Li
- Buildings and Transportation Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Jihua Chen
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Monojoy Goswami
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Micholas Dean Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Loukas Petridis
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Soydan Ozcan
- Manufacturing Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Jeremy C Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
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65
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Prabhu J, Frigerio M, Petretto E, Campomanes P, Salentinig S, Vanni S. A Coarse-Grained SPICA Makeover for Solvated and Bare Sodium and Chloride Ions. J Chem Theory Comput 2024; 20:7624-7634. [PMID: 39160094 PMCID: PMC11391577 DOI: 10.1021/acs.jctc.4c00529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Aqueous ionic solutions are pivotal in various scientific domains due to their natural prevalence and vital roles in biological and chemical processes. Molecular dynamics has emerged as an effective methodology for studying the dynamic behavior of these systems. While all-atomistic models have made significant strides in accurately representing and simulating these ions, the challenge persists in achieving precise models for coarse-grained (CG) simulations. Our study introduces two optimized models for sodium and chloride ions within the nonpolarizable surface property fitting coarse-grained force field (SPICA-FF) framework. The two models represent solvated ions, such as the original FF model, and unsolvated or bare ions. The nonbonded Lennard-Jones interactions were reparameterized to faithfully reproduce bulk properties, including density and surface tension, in sodium chloride solutions at varying concentrations. Notably, these optimized models replicate experimental surface tensions at high ionic strengths, a property not well-captured by the ions of the original model in the SPICA-FF. The optimized unsolvated model also proved successful in reproducing experimental osmotic pressure. Additionally, the newly reparameterized ion models capture hydrophobic interactions within sodium chloride solutions and show qualitative agreement when modeling structural changes in phospholipid bilayers, aligning with experimental observations. For aqueous solutions, these optimized models promise a more precise representation of the ion behavior.
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Affiliation(s)
- Janak Prabhu
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Matteo Frigerio
- Department of Chemistry, University of Fribourg, 1700 Fribourg, Switzerland
| | - Emanuele Petretto
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Pablo Campomanes
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Stefan Salentinig
- Department of Chemistry, University of Fribourg, 1700 Fribourg, Switzerland
- National Center of Competence in Research Bio-inspired Materials, University of Fribourg, 1700 Fribourg, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- National Center of Competence in Research Bio-inspired Materials, University of Fribourg, 1700 Fribourg, Switzerland
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66
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Mulashkina TI, Kulakova AM, Khrenova MG. Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study. J Chem Inf Model 2024. [PMID: 39255503 DOI: 10.1021/acs.jcim.4c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
The occurrence of organophosphorus compounds, pesticides, and flame-retardants in wastes is an emerging ecological problem. Bacterial phosphotriesterases are capable of hydrolyzing some of them. We utilize modern molecular modeling tools to study the hydrolysis mechanism of organophosphorus compounds with good and poor leaving groups by phosphotriesterase from Pseudomonas diminuta (Pd-PTE). We compute Gibbs energy profiles for enzymes with different cations in the active site: native Zn2+cations and Co2+cations, which increase the steady-state rate constant. Hydrolysis occurs in two elementary steps via an associative mechanism and formation of the pentacoordinated intermediate. The first step, a nucleophilic attack, occurs with a low energy barrier independently of the substrate. The second step has a low energy barrier and considerable stabilization of products for substrates with good leaving groups. For substrates with poor leaving groups, the reaction products are destabilized relative to the ES complex that suppresses the reaction. The reaction proceeds with low energy barriers for substrates with good leaving groups with both Zn2+and Co2+cations in the active site; thus, the product release is likely to be a limiting step. Electron density and geometry analysis of the QM/MM MD trajectories of the intermediate states with all considered compounds allow us to discriminate substrates by their ability to be hydrolyzed by the Pd-PTE. For hydrolyzable substrates, the cleaving bond between a phosphorus atom and a leaving group is elongated, and electron density depletion is observed on the Laplacian of electron density maps.
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Affiliation(s)
- Tatiana I Mulashkina
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna M Kulakova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
- Bach Institute of Biochemistry, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia
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67
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Bykhovskaia M. Dynamic formation of the protein-lipid prefusion complex. Biophys J 2024:S0006-3495(24)00601-5. [PMID: 39257001 DOI: 10.1016/j.bpj.2024.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 08/12/2024] [Accepted: 09/06/2024] [Indexed: 09/12/2024] Open
Abstract
Synaptic vesicles (SVs) fuse with the presynaptic membrane (PM) to release neuronal transmitters. The SV protein synaptotagmin 1 (Syt1) serves as a Ca2+ sensor for evoked fusion. Syt1 is thought to trigger fusion by penetrating the PM upon Ca2+ binding; however, the mechanistic detail of this process is still debated. Syt1 interacts with the SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) complex, a coiled-coil four-helical bundle that enables the SV-PM attachment. The SNARE-associated protein complexin (Cpx) promotes Ca2+-dependent fusion, possibly interacting with Syt1. We employed all-atom molecular dynamics to investigate the formation of the Syt1-SNARE-Cpx complex interacting with the lipid bilayers of the PM and SVs. Our simulations demonstrated that the PM-Syt1-SNARE-Cpx complex can transition to a "dead-end" state, wherein Syt1 attaches tightly to the PM but does not immerse into it, as opposed to a prefusion state, which has the tips of the Ca2+-bound C2 domains of Syt1 inserted into the PM. Our simulations unraveled the sequence of Syt1 conformational transitions, including the simultaneous docking of Syt1 to the SNARE-Cpx bundle and the PM, followed by Ca2+ chelation and the penetration of the tips of Syt1 domains into the PM, leading to the prefusion state of the protein-lipid complex. Importantly, we found that direct Syt1-Cpx interactions are required to promote these transitions. Thus, we developed the all-atom dynamic model of the conformational transitions that lead to the formation of the prefusion PM-Syt1-SNARE-Cpx complex. Our simulations also revealed an alternative dead-end state of the protein-lipid complex that can be formed if this pathway is disrupted.
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68
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Rai P, Clark CJ, Womack CB, Dearing C, Thammathong J, Norman DD, Tigyi GJ, Sen S, Bicker K, Weissmiller AM, Banerjee S. Novel Autotaxin Inhibitor ATX-1d Significantly Enhances Potency of Paclitaxel-An In Silico and In Vitro Study. Molecules 2024; 29:4285. [PMID: 39339280 PMCID: PMC11434342 DOI: 10.3390/molecules29184285] [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: 08/07/2024] [Revised: 09/05/2024] [Accepted: 09/06/2024] [Indexed: 09/30/2024] Open
Abstract
The development of drug resistance in cancer cells poses a significant challenge for treatment, with nearly 90% of cancer-related deaths attributed to it. Over 50% of ovarian cancer patients and 30-40% of breast cancer patients exhibit resistance to therapies such as Taxol. Previous literature has shown that cytotoxic cancer therapies and ionizing radiation damage tumors, prompting cancer cells to exploit the autotaxin (ATX)-lysophosphatidic acid (LPA)-lysophosphatidic acid receptor (LPAR) signaling axis to enhance survival pathways, thus reducing treatment efficacy. Therefore, targeting this signaling axis has become a crucial strategy to overcome some forms of cancer resistance. Addressing this challenge, we identified and assessed ATX-1d, a novel compound targeting ATX, through computational methods and in vitro assays. ATX-1d exhibited an IC50 of 1.8 ± 0.3 μM for ATX inhibition and demonstrated a significant binding affinity for ATX, as confirmed by MM-GBSA, QM/MM-GBSA, and SAPT in silico methods. ATX-1d significantly amplified the potency of paclitaxel, increasing its effectiveness tenfold in 4T1 murine breast carcinoma cells and fourfold in A375 human melanoma cells without inducing cytotoxic effects as a single agent.
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Affiliation(s)
- Prateek Rai
- Molecular Biosciences, Middle Tennessee State University, Murfreesboro, TN 37132, USA
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Christopher J Clark
- Molecular Biosciences, Middle Tennessee State University, Murfreesboro, TN 37132, USA
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Carl B Womack
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Curtis Dearing
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Joshua Thammathong
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Derek D Norman
- Department of Physiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Gábor J Tigyi
- Department of Physiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Subhabrata Sen
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Deemed to be University, Dadri 201314, UP, India
| | - Kevin Bicker
- Molecular Biosciences, Middle Tennessee State University, Murfreesboro, TN 37132, USA
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - April M Weissmiller
- Molecular Biosciences, Middle Tennessee State University, Murfreesboro, TN 37132, USA
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Souvik Banerjee
- Molecular Biosciences, Middle Tennessee State University, Murfreesboro, TN 37132, USA
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, TN 37132, USA
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69
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Urwin DJ, Tran E, Alexandrova AN. Relative genotoxicity of polycyclic aromatic hydrocarbons inferred from free energy perturbation approaches. Proc Natl Acad Sci U S A 2024; 121:e2322155121. [PMID: 39226345 PMCID: PMC11406254 DOI: 10.1073/pnas.2322155121] [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: 01/08/2024] [Accepted: 06/27/2024] [Indexed: 09/05/2024] Open
Abstract
Utilizing molecular dynamics and free energy perturbation, we examine the relative binding affinity of several covalent polycyclic aromatic hydrocarbon - DNA (PAH-DNA) adducts at the central adenine of NRAS codon-61, a mutational hotspot implicated in cancer risk. Several PAHs classified by the International Agency for Research on Cancer as probable, possible, or unclassifiable as to carcinogenicity are found to have greater binding affinity than the known carcinogen, benzo[a]pyrene (B[a]P). van der Waals interactions between the intercalated PAH and neighboring nucleobases, and minimal disruption of the DNA duplex drive increases in binding affinity. PAH-DNA adducts may be repaired by global genomic nucleotide excision repair (GG-NER), hence we also compute relative free energies of complexation of PAH-DNA adducts with RAD4-RAD23 (the yeast ortholog of human XPC-RAD23) which constitutes the recognition step in GG-NER. PAH-DNA adducts exhibiting the greatest DNA binding affinity also exhibit the least RAD4-RAD23 complexation affinity and are thus predicted to resist the GG-NER machinery, contributing to their genotoxic potential. In particular, the fjord region PAHs dibenzo[a,l]pyrene, benzo[g]chrysene, and benzo[c]phenanthrene are found to have greater binding affinity while having weaker RAD4-RAD23 complexation affinity than their respective bay region analogs B[a]P, chrysene, and phenanthrene. We also find that the bay region PAHs dibenzo[a,j]anthracene, dibenzo[a,c]anthracene, and dibenzo[a,h]anthracene exhibit greater binding affinity and weaker RAD4-RAD23 complexation affinity than B[a]P. Thus, the study of PAH genotoxicity likely needs to be substantially broadened, with implications for public policy and the health sciences. This approach can be broadly applied to assess factors contributing to the genotoxicity of other unclassified compounds.
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Affiliation(s)
- Derek J Urwin
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095
| | - Elise Tran
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095
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70
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Kim S. All-Atom Membrane Builder via Multiscale Simulation. J Chem Inf Model 2024. [PMID: 39250520 DOI: 10.1021/acs.jcim.4c01059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
I present an automated and flexible tool designed for constructing bilayer membranes at all-atom (AA) resolution. The builder initiates the construction and equilibration of bilayer membranes at Martini coarse-grained (CG) resolution, followed by resolution enhancement to the atomic level using the accompanying backmapping tool. Notably, this tool enables users to create bilayer membranes with user-defined lipid compositions and protein structures, while also offering the flexibility to accommodate new lipid types. To assess the simplicity and robustness of the tool, I demonstrate the construction of several membranes incorporating protein structures. The tool is freely available at github.com/ksy141/mstool.
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Affiliation(s)
- Siyoung Kim
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
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71
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Chen R, Liu H, Meng W, Sun J. Analysis of action of 1,4-naphthoquinone scaffold-derived compounds against acute myeloid leukemia based on network pharmacology, molecular docking and molecular dynamics simulation. Sci Rep 2024; 14:21043. [PMID: 39251712 PMCID: PMC11385794 DOI: 10.1038/s41598-024-70937-y] [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: 01/29/2024] [Accepted: 08/22/2024] [Indexed: 09/11/2024] Open
Abstract
1,4-Naphthoquinone scaffold-derived compounds has shown considerable pharmacological properties against cancer, including acute myeloid leukemia (AML) However, its impact and mechanisms in AML are uncertain. In this study, the mechanisms of 1,4-naphthoquinone scaffold-derived compounds against AML were investigated via network pharmacology, molecular docking and molecular dynamics simulation. ASINEX database was used to collect the 1,4-naphthoquinone scaffold-derived compounds, and compounds were extracted from the software to evaluate their drug similarity and toxicity. The potential targets of compounds were retrieved from the SwissTargetPrediction Database and the Similarity Ensemble Approach Database, while the potential targets of AML were obtained from the GeneCards databases and Gene Expression Omnibus. The STRING database was used to construct a protein-protein interaction (PPI) network, topologically and Cyto Hubb plugin of Cytoscape screen the central targets. After selecting the potential key targets, the gene ontology (GO) function annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed for the intersection targets, and a network map of "compounds-potential targets-pathway-disease" were constructed. Molecular docking of the compounds with the core target was performed, and core target with the strongest binding force and 1,4-naphthoquinone scaffold-derived compounds was selected for further molecular dynamics simulation and further molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) approach verification. In addition, the Bloodspot database was applied to perform the overall survival of core targets. A total of 19 1,4-naphthoquinone scaffold-derived compounds were chosen out, and then 836 targets of compounds, 96 intersection targets of AML were screened. Core targets include STAT3, TLR4, HSP90AA1, JUN, MMP9, PTPRC, JAK2, PTGS2, KIT and CSF1R. GO functional enrichment analysis revealed that 90 biological processes, 10 cell components and 12 molecular functions were enriched while KEGG pathway enrichment analysis revealed 34 enriched signaling pathways. Analysis of KEGG enrichment hinted that these 10 core genes were located in the pathways in cancer, suggesting that 1,4-naphthoquinone scaffold-derived compounds had potential activity against AML. Molecular docking analysis revealed that the binding energies between 1,4-naphthoquinone scaffold-derived compounds and the core proteins were all higher than - 6 kcal/mol, indicating that the 10 core targets all had strong binding ability with compounds. Moreover, a good binding capacity was inferred from molecular dynamics simulations between compound 7 and MMP9. The total binding free energy calculated using the MM/GBSA approach revealed values of - 6356.865 kcal/mol for the MMP9-7 complex. In addition, Bloodspot database results exhibited that HSP90AA1, MMP9 and PTPRC were associated with overall survival. The findings provide foundations for future studies into the interaction underlying the anti-AML potential of compounds with 1,4-naphthoquinone-based scaffold structures. Compounds with 1,4-naphthoquinone-based scaffold structures exhibits considerable potential in mitigating and treating AML through multiple targets and pathways.
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Affiliation(s)
- Rong Chen
- Department of Oncology, Lishui People's Hospital, Lishui, 323000, China
| | - Hengfang Liu
- Department of Hematology Oncology, Taizhou Municipal Hospital, Taizhou, 318000, China
| | - Weikang Meng
- Department of Hematology Oncology, Taizhou Municipal Hospital, Taizhou, 318000, China
| | - Jingyu Sun
- Department of Hematology Oncology, Taizhou Municipal Hospital, Taizhou, 318000, China.
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72
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Weerakoon D, Marzinek JK, Pedebos C, Bond PJ, Khalid S. Polymyxin B1 in the E. coli inner membrane: a complex story of protein and lipopolysaccharide mediated insertion. J Biol Chem 2024:107754. [PMID: 39260694 DOI: 10.1016/j.jbc.2024.107754] [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: 02/10/2024] [Revised: 08/21/2024] [Accepted: 08/29/2024] [Indexed: 09/13/2024] Open
Abstract
The rise in multi-drug resistant Gram-negative bacterial infections has led to an increased need for 'last-resort' antibiotics such as polymyxins. However, the emergence of polymyxin-resistant strains threatens to bring about a post-antibiotic era. Thus, there is a need to develop new polymyxin-based antibiotics, but a lack of knowledge of the mechanism of action of polymyxins hinders such efforts. It has recently been suggested that polymyxins induce cell lysis of the Gram-negative bacterial inner membrane (IM) by targeting trace amounts of lipopolysaccharide (LPS) localized there. We use multiscale molecular dynamics (MD) including long-timescale coarse-grained (CG) and all-atom (AA) simulations to investigate the interactions of polymyxin B1 (PMB1) with bacterial IM models containing phospholipids (PLs), small quantities of LPS, and IM proteins. LPS was observed to (transiently) phase separate from PLs at multiple LPS concentrations, and associate with proteins in the IM. PMB1 spontaneously inserted into the IM and localized at the LPS-PL interface, where it cross-linked lipid headgroups via hydrogen bonds, sampling a wide range of interfacial environments. In the presence of membrane proteins, a small number of PMB1 molecules formed interactions with them, in a manner that was modulated by local LPS molecules. Electroporation-driven translocation of PMB1 via water-filled pores was favored at the protein-PL interface, supporting the 'destabilizing' role proteins may have within the IM. Overall, this in-depth characterization of PMB1 modes of interaction reveals how small amounts of mislocalized LPS may play a role in pre-lytic targeting and provides insights that may facilitate rational improvement of polymyxin-based antibiotics.
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Affiliation(s)
- Dhanushka Weerakoon
- School of Chemistry, University of Southampton, SO17 1BJ, UK; Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Jan K Marzinek
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Conrado Pedebos
- Department of Biochemistry, University of Oxford, OX1 3QU, UK; Programa de Pós-Graduação em Biociências (PPGBio), Universidade Federal de Ciências da Saudé de Porto Alegre - UFCSPA, Brazil
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, OX1 3QU, UK
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73
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Alkhatabi HA, Alatyb HN. Pharmacophore-Based Study: An In Silico Perspective for the Identification of Potential New Delhi Metallo-β-lactamase-1 (NDM-1) Inhibitors. Pharmaceuticals (Basel) 2024; 17:1183. [PMID: 39338345 PMCID: PMC11435111 DOI: 10.3390/ph17091183] [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: 08/06/2024] [Revised: 08/29/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024] Open
Abstract
In the ongoing battle against antibiotic-resistant bacteria, New Delhi metallo-β-lactamase-1 (NDM-1) has emerged as a significant therapeutic challenge due to its ability to confer resistance to a broad range of β-lactam antibiotics. This study presents a pharmacophore-based virtual screening, docking, and molecular dynamics simulation approach for the identification of potential inhibitors targeting NDM-1, a critical enzyme associated with antibiotic resistance. Through the generation of a pharmacophore model and subsequent virtual screening of compound libraries, candidate molecules (ZINC29142850 (Z1), ZINC78607001 (Z2), and ZINC94303138 (Z3)) were prioritized based on their similarity to known NDM-1 binder (hydrolyzed oxacillin (0WO)). Molecular docking studies further elucidated the binding modes and affinities of the selected compounds towards the active site of NDM-1. These compounds demonstrated superior binding affinities to the enzyme compared to a control compound (-7.30 kcal/mol), with binding scores of -7.13, -7.92, and -8.10 kcal/mol, respectively. Binding interactions within NDM-1's active site showed significant interactions with critical residues such as His250, Asn220, and Trp93 for these compounds. Subsequent molecular dynamics simulations were conducted to assess the stability of the ligand-enzyme complexes, showing low root mean square deviation (RMSD) values between 0.5 and 0.7 nm for Z1, Z2, which indicate high stability. Z2's compactness in principal component analysis (PCA) suggests that it can stabilize particular protein conformations more efficiently. Z2 displays a very cohesive landscape with a notable deep basin, suggesting a very persistent conformational state induced by the ligand, indicating robust binding and perhaps efficient inhibition. Z2 demonstrates the highest binding affinity among the examined compounds with a binding free energy of -25.68 kcal/mol, suggesting that it could offer effective inhibition of NDM-1. This study highlights the efficacy of computational tools in identifying novel antimicrobial agents against resistant bacteria, accelerating drug discovery processes.
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Affiliation(s)
- Heba Ahmed Alkhatabi
- Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Hematology Research Unit (HRU), King Fahd Medical Research Center (KFMRC), Jeddah 80200, Saudi Arabia
| | - Hisham N. Alatyb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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74
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Quintana-Feliciano R, Kottur J, Ni M, Ghosh R, Salas-Estrada L, Ahlsen G, Rechkoblit O, Shapiro L, Filizola M, Fang G, Aggarwal AK. Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation. Nat Commun 2024; 15:7839. [PMID: 39244607 PMCID: PMC11380664 DOI: 10.1038/s41467-024-52130-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 08/27/2024] [Indexed: 09/09/2024] Open
Abstract
Burkholderia cenocepacia is an opportunistic and infective bacterium containing an orphan DNA methyltransferase called M.BceJIV with roles in regulating gene expression and motility of the bacterium. M.BceJIV recognizes a GTWWAC motif (where W can be an adenine or a thymine) and methylates N6 of the adenine at the fifth base position. Here, we present crystal structures of M.BceJIV/DNA/sinefungin ternary complex and allied biochemical, computational, and thermodynamic analyses. Remarkably, the structures show not one, but two DNA substrates bound to the M.BceJIV dimer, with each monomer contributing to the recognition of two recognition sequences. We also show that methylation at the two recognition sequences occurs independently, and that the GTWWAC motifs are enriched in intergenic regions in the genomes of B. cenocepacia strains. We further computationally assess the interactions underlying the affinities of different ligands (SAM, SAH, and sinefungin) for M.BceJIV, as a step towards developing selective inhibitors for limiting B. cenocepacia infection.
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Affiliation(s)
- Richard Quintana-Feliciano
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jithesh Kottur
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
- Department of Antiviral Drug Research, Institute of Advanced Virology, Thiruvananthapuram, Kerala, India.
| | - Mi Ni
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Rikhia Ghosh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Leslie Salas-Estrada
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Goran Ahlsen
- Department of Biochemistry and Molecular Biophysics Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Olga Rechkoblit
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Aneel K Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
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75
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Fan C, Cowgill J, Howard RJ, Lindahl E. Divergent mechanisms of steroid inhibition in the human ρ1 GABA A receptor. Nat Commun 2024; 15:7795. [PMID: 39242530 PMCID: PMC11379708 DOI: 10.1038/s41467-024-51904-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 08/19/2024] [Indexed: 09/09/2024] Open
Abstract
ρ-type γ-aminobutyric acid-A (GABAA) receptors are widely distributed in the retina and brain, and are potential drug targets for the treatment of visual, sleep and cognitive disorders. Endogenous neuroactive steroids including β-estradiol and pregnenolone sulfate negatively modulate the function of ρ1 GABAA receptors, but their inhibitory mechanisms are not clear. By combining five cryo-EM structures with electrophysiology and molecular dynamics simulations, we characterize binding sites and negative modulation mechanisms of β-estradiol and pregnenolone sulfate at the human ρ1 GABAA receptor. β-estradiol binds in a pocket at the interface between extracellular and transmembrane domains, apparently specific to the ρ subfamily, and disturbs allosteric conformational transitions linking GABA binding to pore opening. In contrast, pregnenolone sulfate binds inside the pore to block ion permeation, with a preference for activated structures. These results illuminate contrasting mechanisms of ρ1 inhibition by two different neuroactive steroids, with potential implications for subtype-specific gating and pharmacological design.
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Affiliation(s)
- Chen Fan
- Dept. of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
- Dept. of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - John Cowgill
- Dept. of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Rebecca J Howard
- Dept. of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.
- Dept. of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.
| | - Erik Lindahl
- Dept. of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.
- Dept. of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.
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76
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Kyobe S, Mwesigwa S, Nkurunungi G, Retshabile G, Egesa M, Katagirya E, Amujal M, Mlotshwa BC, Williams L, Sendagire H, On Behalf Of The CAfGEN Consortium, Kiragga D, Mardon G, Matshaba M, Hanchard NA, Kyosiimire-Lugemwa J, Robinson D. Identification of a Clade-Specific HLA-C*03:02 CTL Epitope GY9 Derived from the HIV-1 p17 Matrix Protein. Int J Mol Sci 2024; 25:9683. [PMID: 39273630 PMCID: PMC11395705 DOI: 10.3390/ijms25179683] [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: 10/07/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 09/15/2024] Open
Abstract
Efforts towards an effective HIV-1 vaccine have remained mainly unsuccessful. There is increasing evidence for a potential role of HLA-C-restricted CD8+ T cell responses in HIV-1 control, including our recent report of HLA-C*03:02 among African children. However, there are no documented optimal HIV-1 CD8+ T cell epitopes restricted by HLA-C*03:02; additionally, the structural influence of HLA-C*03:02 on epitope binding is undetermined. Immunoinformatics approaches provide a fast and inexpensive method to discover HLA-restricted epitopes. Here, we employed immunopeptidomics to identify HLA-C*03:02 CD8+ T cell epitopes. We identified a clade-specific Gag-derived GY9 (GTEELRSLY) HIV-1 p17 matrix epitope potentially restricted to HLA-C*03:02. Residues E62, T142, and E151 in the HLA-C*03:02 binding groove and positions p3, p6, and p9 on the GY9 epitope are crucial in shaping and stabilizing the epitope binding. Our findings support the growing evidence of the contribution of HLA-C molecules to HIV-1 control and provide a prospect for vaccine strategies.
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Affiliation(s)
- Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala P.O. Box 7072, Uganda
| | - Savannah Mwesigwa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala P.O. Box 7072, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala P.O. Box 7072, Uganda
| | - Gyaviira Nkurunungi
- The Medical Research Council/Uganda Virus Research Institute & London School Hygine Tropical Medicine Uganda Research Unit, Entebbe P.O. Box 49, Uganda
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street London, London WC1E 7HT, UK
| | - Gaone Retshabile
- Department of Biological Sciences, University of Botswana, Gaborone Private Bag UB 0022, Botswana
| | - Moses Egesa
- The Medical Research Council/Uganda Virus Research Institute & London School Hygine Tropical Medicine Uganda Research Unit, Entebbe P.O. Box 49, Uganda
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street London, London WC1E 7HT, UK
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala P.O. Box 7072, Uganda
| | - Marion Amujal
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala P.O. Box 7072, Uganda
| | - Busisiwe C Mlotshwa
- Department of Biological Sciences, University of Botswana, Gaborone Private Bag UB 0022, Botswana
| | - Lesedi Williams
- Department of Biological Sciences, University of Botswana, Gaborone Private Bag UB 0022, Botswana
| | - Hakim Sendagire
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala P.O. Box 7072, Uganda
| | | | - Dithan Kiragga
- Baylor College of Medicine Children's Foundation, Kampala P.O. Box 72052, Uganda
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mogomotsi Matshaba
- Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone Private Bag BR 129, Botswana
| | - Neil A Hanchard
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA
| | - Jacqueline Kyosiimire-Lugemwa
- The Medical Research Council/Uganda Virus Research Institute & London School Hygine Tropical Medicine Uganda Research Unit, Entebbe P.O. Box 49, Uganda
| | - David Robinson
- Department of Chemistry and Forensics, School of Science and Technology, Nottingham Trent University Clifton Lane, Nottingham NG11 8NS, UK
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Costanzo A, Fata F, Freda I, De Sciscio ML, Gugole E, Bulfaro G, Di Renzo M, Barbizzi L, Exertier C, Parisi G, D'Abramo M, Vallone B, Savino C, Montemiglio LC. Binding of steroid substrates reveals the key to the productive transition of the cytochrome P450 OleP. Structure 2024; 32:1465-1476.e3. [PMID: 38971159 DOI: 10.1016/j.str.2024.06.005] [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: 01/05/2024] [Revised: 05/08/2024] [Accepted: 06/11/2024] [Indexed: 07/08/2024]
Abstract
OleP is a bacterial cytochrome P450 involved in oleandomycin biosynthesis as it catalyzes regioselective epoxidation on macrolide intermediates. OleP has recently been reported to convert lithocholic acid (LCA) into murideoxycholic acid through a highly regioselective reaction and to unspecifically hydroxylate testosterone (TES). Since LCA and TES mainly differ by the substituent group at the C17, here we used X-ray crystallography, equilibrium binding assays, and molecular dynamics simulations to investigate the molecular basis of the diverse reactivity observed with the two steroids. We found that the differences in the structure of TES and LCA affect the capability of these molecules to directly form hydrogen bonds with N-terminal residues of OleP internal helix I. The establishment of these contacts, by promoting the bending of helix I, fosters an efficient trigger of the open-to-closed structural transition that occurs upon substrate binding to OleP and contributes to the selectivity of the subsequent monooxygenation reaction.
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Affiliation(s)
- Antonella Costanzo
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy
| | - Francesca Fata
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
| | - Ida Freda
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Maria Laura De Sciscio
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Elena Gugole
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
| | - Giovanni Bulfaro
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; Takis Biotech, Via di Castel Romano 100, 00128 Rome, Italy
| | - Matteo Di Renzo
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Luca Barbizzi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Cécile Exertier
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy
| | - Giacomo Parisi
- Department of Basic and Applied Sciences for Engineering (SBAI), Sapienza, University of Rome, Via Antonio Scarpa, 16, 00161 Rome, Italy
| | - Marco D'Abramo
- Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy; Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy.
| | - Carmelinda Savino
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy.
| | - Linda Celeste Montemiglio
- Institute of Molecular Biology and Pathology c/o Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza, University of Rome, National Research Council, P.le Aldo Moro, 5, 00185 Rome, Italy.
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78
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Boakye A, Seidu MP, Adomako A, Laryea MK, Borquaye LS. Marine-Derived Furanones Targeting Quorum-Sensing Receptors in Pseudomonas aeruginosa: Molecular Insights and Potential Mechanisms of Inhibition. Bioinform Biol Insights 2024; 18:11779322241275843. [PMID: 39246683 PMCID: PMC11378241 DOI: 10.1177/11779322241275843] [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: 03/02/2024] [Accepted: 07/30/2024] [Indexed: 09/10/2024] Open
Abstract
The quorum-sensing (QS) machinery in disease-causing microorganisms is critical in developing antibiotic resistance. In Pseudomonas aeruginosa, QS is involved in biofilm formation, virulence factors production, and general tolerance to antimicrobials. Owing to the major role QS plays, interference in the process is probably a facile route to overcome antimicrobial resistance. Some furanone-derived compounds from marine sources have shown promising anti-QS activity. However, their protein targets and potential mechanisms of action have not been explored. To elucidate their potential protein targets in this study, marine metabolites with furanone backbones similar to their cognitive autoinducers (AIs) were screened against various QS receptors (LasR, RhlR, and PqsR) using molecular docking and molecular dynamics (MD) simulation techniques. The order by which the compounds bind to the receptors follows LasR > RhlR > PqsR. Compounds exhibited remarkable stability against LasR and RhlR, likely because the AIs of these receptors are structural analogs of furanones. Furanones with shorter alkyl side chains bound strongly against RhlR. The presence of halogens improved binding against various receptors. PqsR, with its hydrophobic-binding site and structurally different AIs, showed weaker binding. This study provides a molecular basis for the design of potent antagonists against QS receptors using marine-derived furanones.
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Affiliation(s)
- Aaron Boakye
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Alice Adomako
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael Konney Laryea
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Lawrence Sheringham Borquaye
- Department of Chemistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Central Laboratory, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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79
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Wang Q, Schirmer A, Paula S, Jayasinghe M. Druglike Molecules Binding to Large Membrane Proteins: Absolute Binding Free Energy Computation. J Phys Chem B 2024; 128:8332-8343. [PMID: 39189334 DOI: 10.1021/acs.jpcb.4c02534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
In this research, we employed the alchemical double-decoupling method alongside restraining potentials, coupled with the FEPMD method, to ascertain the standard binding free energy of a drug-like molecule termed BHQ and three analogous compounds engineered with progressive addition of bulky para-alkyl groups binding to SERCA (Ca2+-ATPase of skeletal muscle sarcoplasmic reticulum). Integral transmembrane proteins represent crucial drug targets in numerous therapeutic interventions, presenting computational challenges due to their considerable system sizes. Our approach integrated the generalized born potential method and the spherical solvent boundary potential method, allowing us to explicitly focus on the active binding site while treating the remainder of the system implicitly. We evaluated contributions to the standard binding free energy from distinct interaction potentials: electrostatic, repulsive, dispersive, and restraining potentials, computed separately. The resulting absolute binding free energy of BHQ (11.63 kcal/mol) closely aligns with experimental measurements (10.56 kcal/mol). Notably, an accurate estimation of the absolute binding free energy was achieved for the simplest analog, created with the addition of a single para-methyl group. However, the analog with two para-methyl groups exhibited the highest binding free energy, which disagreed with experimental results. Determining the binding free energy of the BHQ analog engineered with three para-methyl groups presented challenges in convergence and resulted in the lowest free energy among the three.
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Affiliation(s)
- Qi Wang
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Andrew Schirmer
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Stefan Paula
- Chemistry Department, California State University Sacramento, 6000 J Street, Sacramento, California 95819, United States
| | - Manori Jayasinghe
- Department of Mathematics, Physics and Computer Science, University of Cincinnati Blue Ash College, Blue Ash, Ohio 45236, United States
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80
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Boittier E, Töpfer K, Devereux M, Meuwly M. Kernel-Based Minimal Distributed Charges: A Conformationally Dependent ESP-Model for Molecular Simulations. J Chem Theory Comput 2024. [PMID: 39230188 DOI: 10.1021/acs.jctc.4c00759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
A kernel-based method (kernelized minimal distributed charge model (kMDCM)) to represent the molecular electrostatic potential (ESP) in terms of off-center point charges is introduced. The positions of the charges adapt to the molecular geometry and allow the description of intramolecular charge flow. Using Gaussian kernels and atom-atom distances as the features, the ESPs for water and methanol are shown to improve by at least a factor of 2 compared with point charge models fit to an ensemble of structures. The conformationally fluctuating molecular dipole moment of water is reproduced almost twice as accurately using kMDCM compared with static PCs, despite not fitting to the dipole directly. The role of hyperparameters in the kernelization is investigated and their implication on model performance and simulation stability is discussed. Combining kMDCM for the electrostatics and reproducing kernels for the bonded terms allows energy-conserving simulations of 2000 water molecules with periodic boundary conditions on the nanosecond time scale. These MD simulations sample geometries outside the training set but remain stable, which demonstrates the robustness of the model and its implementation.
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Affiliation(s)
- Eric Boittier
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Mike Devereux
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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81
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Villalaín J. Bisphenol F and Bisphenol S in a Complex Biomembrane: Comparison with Bisphenol A. J Xenobiot 2024; 14:1201-1220. [PMID: 39311147 PMCID: PMC11417855 DOI: 10.3390/jox14030068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/24/2024] [Accepted: 09/01/2024] [Indexed: 09/26/2024] Open
Abstract
Bisphenols are a group of endocrine-disrupting chemicals used worldwide for the production of plastics and resins. Bisphenol A (BPA), the main bisphenol, exhibits many unwanted effects. BPA has, currently, been replaced with bisphenol F (BPF) and bisphenol S (BPS) in many applications in the hope that these molecules have a lesser effect on metabolism than BPA. Since bisphenols tend to partition into the lipid phase, their place of choice would be the cellular membrane. In this paper, I carried out molecular dynamics simulations to compare the localization and interactions of BPA, BPF, and BPS in a complex membrane. This study suggests that bisphenols tend to be placed at the membrane interface, they have no preferred orientation inside the membrane, they can be in the monomer or aggregated state, and they affect the biophysical properties of the membrane lipids. The properties of bisphenols can be attributed, at least in part, to their membranotropic effects and to the modulation of the biophysical membrane properties. The data support that both BPF and BPS, behaving in the same way in the membrane as BPA and with the same capacity to accumulate in the biological membrane, are not safe alternatives to BPA.
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Affiliation(s)
- José Villalaín
- Institute of Research, Development, and Innovation in Healthcare Biotechnology (IDiBE), Universidad "Miguel Hernández", E-03202 Elche, Alicante, Spain
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82
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Coppola F, Jafari R, McReynolds KD, Král P. Sulfoglycodendron Antivirals with Scalable Architectures and Activities. J Chem Inf Model 2024. [PMID: 39230262 DOI: 10.1021/acs.jcim.4c00541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Many viruses initiate their cell-entry by binding their multisubunit receptors to human heparan sulfate proteoglycans (HSPG) and other molecular components present on cellular membranes. These viral interactions could be blocked and the whole viruses could be eliminated by suitable HSPG-mimetics providing multivalent binding to viral protein receptors. Here, large sulfoglycodendron HSPG-mimetics of different topologies, structures, and sizes were designed to this purpose. Atomistic molecular dynamics simulations were used to examine the ability of these broad-spectrum antivirals to block multiprotein HSPG-receptors in HIV, SARS-CoV-2, HPV, and dengue viruses. To characterize the inhibitory potential of these mimetics, their binding to individual and multiple protein receptors was examined. In particular, vectorial distributions of binding energies between the mimetics and viral protein receptors were introduced and calculated along the simulated trajectories. Space-dependent residual analysis of the mimetic-receptor binding was also performed. This analysis revealed the detailed nature of binding between these antivirals and viral protein receptors and provided evidence that large inhibitors with multivalent binding might act like a molecular glue initiating the self-assembly of protein receptors in enveloped viruses.
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Affiliation(s)
- Francesco Coppola
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Roya Jafari
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Katherine D McReynolds
- Departments of Chemistry, California State University Sacramento, 6000 J Street, Sacramento, California 95819-6057, United States
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- Departments of Physics, Pharmaceutical Sciences, and Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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83
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Imam MA, Alandijany TA, Felemban HR, Attar RM, Faizo AA, Gattan HS, Dwivedi VD, Azhar EI. Machine learning, network pharmacology, and molecular dynamics reveal potent cyclopeptide inhibitors against dengue virus proteins. Mol Divers 2024:10.1007/s11030-024-10975-w. [PMID: 39227512 DOI: 10.1007/s11030-024-10975-w] [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: 07/12/2024] [Accepted: 08/20/2024] [Indexed: 09/05/2024]
Abstract
The dengue virus is a major global health hazard responsible for an estimated 390 million diseases yearly. This study focused on identifying cyclopeptide inhibitors for envelope structural proteins E, NS1, NS3, and NS5. Additionally, 5579 cyclopeptides were individually screened against the four target proteins using a machine learning-based quantitative structure-activity relationship model. Subsequently, the best 10 cyclopeptides from each protein were selected for molecular docking with their corresponding proteins. Moreover, the protein-peptide complexes with the highest affinity were subjected to a 100-ns molecular dynamics simulation. The protein-protein complexes exhibited superior structural stability and binding interactions. Based on the results of the MD simulation analyses, which included checking values for Root Mean Square Deviation, Root Mean Square Fluctuation, Principal Component Analysis (PCA), free energy landscapes, and energetic components, it was found that NS5-CP03714 complex is more stable and has stronger binding interactions than NS3-CP02054. PCA and free energy landscape plots have confirmed the higher conformational stability of NS5-CP03714. Analysis of the energetic components revealed that NS5-CP03714 (total binding energy = - 47.19 kcal/mol) exhibits more favorable interaction energies and overall binding energy compared to NS3-CP02054 (total binding energy = - 27.36 kcal/mol), suggesting a stronger and more stable formation of the complex. In addition, the drug-target network of two specific peptides (CP02950 and CP05582) and their associated target proteins were analyzed. This analysis revealed valuable information about their ability to target several proteins and their potential for broad-spectrum activity. Additional experimental investigations are necessary to validate these computational results and assess the efficacy of identified peptide inhibitors in biological systems.
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Affiliation(s)
- Mohammed A Imam
- Department of Medical Microbiology and Parasitology, Qunfudah Faculty of Medicine, Umm Al-Qura University, Al-Qunfudah, 21961, Saudi Arabia
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Thamir A Alandijany
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Hashim R Felemban
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Roba M Attar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Biological Sciences/Microbiology, Faculty of Science, University of Jeddah, , 21959, Jeddah, Saudi Arabia
| | - Arwa A Faizo
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Hattan S Gattan
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia
| | - Vivek Dhar Dwivedi
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Saveetha Medical College and Hospitals, Saveetha University, Chennai, India.
- Bioinformatics Research Division, Quanta Calculus, Greater Noida, India.
| | - Esam I Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, 21362, Jeddah, Saudi Arabia.
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, 21362, Jeddah, Saudi Arabia.
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84
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Sha CM, Wang J, Dokholyan NV. Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks. Biophys J 2024; 123:2671-2681. [PMID: 37838833 PMCID: PMC11393712 DOI: 10.1016/j.bpj.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/19/2023] [Accepted: 10/12/2023] [Indexed: 10/16/2023] Open
Abstract
Fast and accurate 3D RNA structure prediction remains a major challenge in structural biology, mostly due to the size and flexibility of RNA molecules, as well as the lack of diverse experimentally determined structures of RNA molecules. Unlike DNA structure, RNA structure is far less constrained by basepair hydrogen bonding, resulting in an explosion of potential stable states. Here, we propose a convolutional neural network that predicts all pairwise distances between residues in an RNA, using a recently described smooth parametrization of Euclidean distance matrices. We achieve high-accuracy predictions on RNAs up to 100 nt in length in fractions of a second, a factor of 107 faster than existing molecular dynamics-based methods. We also convert our coarse-grained machine learning output into an all-atom model using discrete molecular dynamics with constraints. Our proposed computational pipeline predicts all-atom RNA models solely from the nucleotide sequence. However, this method suffers from the same limitation as nucleic acid molecular dynamics: the scarcity of available RNA crystal structures for training.
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Affiliation(s)
- Congzhou M Sha
- Department of Engineering Science and Mechanics, Penn State University, State College, Pennsylvania; Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Jian Wang
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Nikolay V Dokholyan
- Department of Engineering Science and Mechanics, Penn State University, State College, Pennsylvania; Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania; Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania; Department of Chemistry, Penn State University, State College, Pennsylvania; Department of Biomedical Engineering, Penn State University, State College, Pennsylvania.
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85
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Nudrat S, Maity B, Quraishi S, Karankumar I, Kumari K, Jana M, Singha Roy A. Binding Interaction of Coumarin Derivative Daphnetin with Ovalbumin: Molecular Insights into the Complexation Process and Effects of Metal Ions and pH in the Binding and Antifibrillation Studies. Mol Pharm 2024; 21:4708-4725. [PMID: 39115967 DOI: 10.1021/acs.molpharmaceut.4c00675] [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] [Indexed: 08/10/2024]
Abstract
This study investigates the interaction between daphnetin and ovalbumin (OVA) as well as its potential to inhibit OVA fibrillation using both spectroscopic and computational analysis. A moderate binding affinity of 1 × 104 M-1 was observed between OVA and daphnetin, with a static quenched mechanism identified during the fluorescence quenching processes. Metal ions' (Cu2+ and Zn2+) presence led to an increase in the binding affinities of daphnetin toward OVA, mirroring a similar trend observed with the pH variation. Synchronous and 3D fluorescence studies indicated an increase in the polarity of the microenvironment surrounding the Trp residues during binding. Interestingly, circular dichroism and Fourier transform infrared studies showed a significant change in the secondary structure of OVA upon binding with daphnetin. The efficacy of daphnetin in inhibiting protein fibrillation was confirmed through thioflavin T and Congo Red binding assays along with fluorescence microscopic imaging analysis. The thermodynamic assessment showed positive ΔH° [+(29.34 ± 1.526) kJ mol-1] and ΔS° [+(181.726 ± 5.465) J mol-1] values, indicating the presence of the hydrophobic forces, while negative ΔG° signifies spontaneous binding interactions. These experimental findings were further correlated with computational analysis, revealing daphnetin dynamics within the binding site of OVA.
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Affiliation(s)
- Sadia Nudrat
- Department of Chemical and Biological Sciences, National Institute of Technology Meghalaya, Shillong 793003, India
| | - Bilash Maity
- Department of Chemistry, National Institute of Technology Rourkela, Rourkela, Odisha 769008, India
| | - Sana Quraishi
- Department of Chemical and Biological Sciences, National Institute of Technology Meghalaya, Shillong 793003, India
| | - Irungbam Karankumar
- Department of Chemistry, National Institute of Technology Manipur, Imphal, Manipur 795004, India
| | - Kalpana Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Madhurima Jana
- Department of Chemistry, National Institute of Technology Rourkela, Rourkela, Odisha 769008, India
| | - Atanu Singha Roy
- Department of Chemical and Biological Sciences, National Institute of Technology Meghalaya, Shillong 793003, India
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86
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Villalaín J. Location and interaction of idebenone and mitoquinone in a membrane similar to the inner mitochondrial membrane. Comparison with ubiquinone 10. Free Radic Biol Med 2024; 222:211-222. [PMID: 38908803 DOI: 10.1016/j.freeradbiomed.2024.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/10/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
Oxygen is essential for aerobic life on earth but it is also the origin of harmful reactive oxygen species (ROS). Ubiquinone is par excellence the endogenous cellular antioxidant, but a very hydrophobic one. Because of that, other molecules have been envisaged, such as idebenone (IDE) and mitoquinone (MTQ), molecules having the same redox active benzoquinone moiety but higher solubility. We have used molecular dynamics to determine the location and interaction of these molecules, both in their oxidized and reduced forms, with membrane lipids in a membrane similar to that of the mitochondria. Both IDE and reduced IDE (IDOL) are situated near the membrane interface, whereas both MTQ and reduced MTQ (MTQOL) locate in a position adjacent to the phospholipid hydrocarbon chains. The quinone moieties of both ubiquinone 10 (UQ10) and reduced UQ10 (UQOL10) in contraposition to the same moieties of IDE, IDOL, MTQ and MTQOL, located near the membrane interphase, whereas the isoprenoid chains remained at the middle of the hydrocarbon chains. These molecules do not aggregate and their functional quinone moieties are located in the membrane at different depths but near the hydrophobic phospholipid chains whereby protecting them from ROS harmful effects.
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Affiliation(s)
- José Villalaín
- Institute of Research, Development, and Innovation in Healthcare Biotechnology (IDiBE), Universidad "Miguel Hernández", E-03202, Elche, Alicante, Spain.
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87
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Khan MKA, Alouffi S, Ahmad S. Identifying potential inhibitors of C-X-C motif chemokine ligand10 against vitiligo: structure-based virtual screening, molecular dynamics simulation, and principal component analysis. J Biomol Struct Dyn 2024; 42:8045-8062. [PMID: 37565326 DOI: 10.1080/07391102.2023.2242952] [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: 09/09/2022] [Accepted: 07/26/2023] [Indexed: 08/12/2023]
Abstract
The research aims to envisage small molecule inhibitors targeting the C-X-C motif chemokine ligand 10 (CXCL10) of the JAK/STAT pathway. CXCL10 plays a significant role in inducing auto-immunity in vitiligo through JAK/STAT pathway. To accomplish the aim, structure-based virtual screening with fundamental search limits, e.g., molecular weight (MW ≤ 500 Da), hydrogen bond donor (HBD ≤ 5), hydrogen bond acceptor (HBA ≤ 10), and lipophilicity (logP ≤ 5) was used to screen investigational molecules from MCULE database. The SBVS-ligand hits were sifted through toxicity profiling followed by filtration through the Brain or IntestinaL EstimateD-Egg model to check the human intestinal abortion and blood-brain barrier permeation based on two physicochemical properties, including topological surface area and WLOGP. The BOILED-Egg filtered compounds were passed through drug-likeness features other than Pfizer's Lipinski rule of five, viz., Ghose filters, Muegge filters, Egan parameters, and Veber filters, followed by medicinal chemistry's pan assay interference structure and Brenk alert investigation. Chemical compounds that comply with the above ADME descriptors were docked with target protein CXCL10 via AutoDock Vina. The stability of the top two ligand hits was assessed through dynamics simulations of 100 ns and principal component analysis and compared with the reference drugs Baicalein and EGCG. Based on the findings of Gibbs free energy of binding, ADME profiling, medicinal chemistry attributes depiction, root-mean-square deviation, root-mean-square fluctuation, solvent accessible surface area, the free energy of solvation, the radius of gyration, and PCA, MCULE2726078782-0-2 was found better than potential reference drug Baicalein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Sultan Alouffi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Saheem Ahmad
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
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88
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Peng S, Cui G, Li J, Li F, Ji M, Zhang C, Meng T, Li J, Man J. Combined role of stearic acid and maleic anhydride in the development of thermoplastic starch-based materials with ultrahigh ductility and durability. Carbohydr Polym 2024; 339:122296. [PMID: 38823896 DOI: 10.1016/j.carbpol.2024.122296] [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: 03/05/2024] [Revised: 04/30/2024] [Accepted: 05/18/2024] [Indexed: 06/03/2024]
Abstract
The diverse properties reported for starch-based materials indicate their potential for use in the preparation of biodegradable flexible actuators. However, their natural brittleness and lack of durability after modification limit their practical application. Therefore, we propose a strategy for preparing flexible starch-based composites. The results of macro/micro property characterizations and molecular dynamics simulations indicated that using starch, maleic anhydride, and stearic acid (SA), the mobility of the starch chains was enhanced and retrogradation was inhibited through the synergistic effects induced by chain breaking, complex formation with SA, and esterification of the starch molecules. In addition, the elongation at break of the modified starch (MS) reached 2070 %, and considerable ductility (>1000 %) as well as well-complexed structure were maintained after six months. Furthermore, the MS was able to undergo self-healing after fracture or a temperature-controlled stiffness transition. Moreover, it underwent complete degradation in soil within 30 d. Finally, an actuator was prepared by doping the MS with nano-Fe3O4 particles to realize a dual magnetic and optical response. Dynamic monitoring was also achieved based on the electrical signal, thereby demonstrating the broad application scope of this material in the development of biodegradable flexible actuators.
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Affiliation(s)
- Sixian Peng
- Key Laboratory of High Efficiency and Clean Mechanical Manufacture (Ministry of Education), School of Mechanical Engineering, Shandong University, Jinan 250061, China; National Demonstration Center for Experimental Mechanical Engineering Education, Shandong University, Jinan 250061, China
| | - Guanghui Cui
- Key Laboratory of High Efficiency and Clean Mechanical Manufacture (Ministry of Education), School of Mechanical Engineering, Shandong University, Jinan 250061, China; National Demonstration Center for Experimental Mechanical Engineering Education, Shandong University, Jinan 250061, China
| | - Jianfeng Li
- Key Laboratory of High Efficiency and Clean Mechanical Manufacture (Ministry of Education), School of Mechanical Engineering, Shandong University, Jinan 250061, China; National Demonstration Center for Experimental Mechanical Engineering Education, Shandong University, Jinan 250061, China.
| | - Fangyi Li
- Key Laboratory of High Efficiency and Clean Mechanical Manufacture (Ministry of Education), School of Mechanical Engineering, Shandong University, Jinan 250061, China; National Demonstration Center for Experimental Mechanical Engineering Education, Shandong University, Jinan 250061, China
| | - Maocheng Ji
- Key Laboratory of High Efficiency and Clean Mechanical Manufacture (Ministry of Education), School of Mechanical Engineering, Shandong University, Jinan 250061, China; National Demonstration Center for Experimental Mechanical Engineering Education, Shandong University, Jinan 250061, China
| | - Chuanwei Zhang
- College of Mechanical and Electrical Engineering, Qingdao University, Qingdao 266071, China
| | - Tianshuo Meng
- Key Laboratory of High Efficiency and Clean Mechanical Manufacture (Ministry of Education), School of Mechanical Engineering, Shandong University, Jinan 250061, China; National Demonstration Center for Experimental Mechanical Engineering Education, Shandong University, Jinan 250061, China
| | - Jianyong Li
- Key Laboratory of High Efficiency and Clean Mechanical Manufacture (Ministry of Education), School of Mechanical Engineering, Shandong University, Jinan 250061, China; National Demonstration Center for Experimental Mechanical Engineering Education, Shandong University, Jinan 250061, China.
| | - Jia Man
- Key Laboratory of High Efficiency and Clean Mechanical Manufacture (Ministry of Education), School of Mechanical Engineering, Shandong University, Jinan 250061, China; National Demonstration Center for Experimental Mechanical Engineering Education, Shandong University, Jinan 250061, China.
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89
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Kabir MZ, Tayyab H, Erkmen C, Mohamad SB, Uslu B. Comprehensive views toward the biomolecular recognition of an anticancer drug, leflunomide with human serum albumin. J Biomol Struct Dyn 2024; 42:7257-7271. [PMID: 37529911 DOI: 10.1080/07391102.2023.2239931] [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: 01/16/2023] [Accepted: 07/16/2023] [Indexed: 08/03/2023]
Abstract
Biomolecular association of an anticancer drug, leflunomide (LEF) with human serum albumin (HSA), the leading ligands carrier in human circulation was characterized using biophysical (i.e., fluorescence, absorption and voltammetric) methods and computational (i.e., molecular docking and molecular dynamics simulation) techniques. Evaluations of fluorescence, absorption and voltammetric findings endorsed the complex formation between LEF and HSA. An inverse relationship of Stern-Volmer constant-temperature and hyperchromic shift of the protein's absorption signal with addition of LEF confirmed the LEF quenched the HSA fluorescence through static process. Moderate nature of binding strength (binding constant = 2.76-4.77 × 104 M-1) was detected towards the LEF-HSA complexation, while the association process was naturally driven via hydrophobic interactions, van der Waals interactions and hydrogen bonds, as evident from changes in entropy (ΔS= + 19.91 J mol-1 K-1) and enthalpy (ΔH = - 20.09 kJ mol-1), and molecular docking assessments. Spectral analyses of synchronous and three-dimensional fluorescence validated microenvironmental fluctuations near Trp and Tyr residues upon LEF binding to the protein. LEF association with HSA significantly defended temperature-induced destabilization of the protein. Although LEF was found to attach to HSA at Sudlow's sites I and II, but exhibited greater preference toward its site I, as detected by the investigations of competitive site-marker displacement. Molecular dynamics simulation assessment revealed that the complex attained equilibrium throughout simulations, showing the LEF-HSA complex constancy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Zahirul Kabir
- Faculty of Pharmacy, Department of Analytical Chemistry, Ankara University, Ankara, Turkey
| | - Hafsa Tayyab
- Faculty of Science, Bioinformatics Programme, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Cem Erkmen
- Faculty of Pharmacy, Department of Analytical Chemistry, Ankara University, Ankara, Turkey
| | - Saharuddin B Mohamad
- Faculty of Science, Bioinformatics Programme, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
- Centre of Research for Computational Sciences and Informatics for Biology, Bioindustry, Environment, Agriculture and Healthcare, University of Malaya, Kuala Lumpur, Malaysia
| | - Bengi Uslu
- Faculty of Pharmacy, Department of Analytical Chemistry, Ankara University, Ankara, Turkey
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90
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Kathiresan N, Harini K, Veera Ravi A, Veerabharathi P, Pandi S, Ramesh M, Awere CO, Langeswaran K. Deciphering the Potential Therapeutic Effects of Hydnocarpus wightianus Seed Extracts using in vitro and in silico approaches. Microb Pathog 2024; 194:106798. [PMID: 39025383 DOI: 10.1016/j.micpath.2024.106798] [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: 03/04/2024] [Revised: 06/11/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Phytocompounds possess the potential to treat a broad spectrum of disorders due to their remarkable bioactivity. Naturally occurring compounds possess lower toxicity profiles, which making them attractive targets for drug development. Hydnocarpus wightianus seeds were extracted using ethanol, acetone, and hexane solvents. The extracts were evaluated for phytochemicals screening and other therapeutic characteristics, such as free radicals scavenging, anti α-amylase, anti α-glucosidase, and anti-bacterial activities. The ethanolic extract exhibited noteworthy antibacterial characteristics and demonstrated considerable antioxidant, and anti-diabetic effects. The IC50 value of the ethanolic extract for Dpph, α-amylase, and α-glucosidase were found to be 77.299 ± 3.381 μg/mL, 165.56 2.56 μg/mL, and 136.58 ± 5.82 μg/mL, respectively. The ethanolic extract was effective against Methicillin resistant Staphylococcus aureus (26 mm zone of inhibition at 100 μL concentration). Molecular docking investigations revealed the phytoconstituent's inhibitory mechanisms against diabetic, free radicals, and bacterial activity. Docking score for phytocompounds against targeted protein varies from -7.2 to -5.1 kcal/mol. The bioactive compounds present in the ethanolic extract were identified by Gas chromatography/Mass spectrometry analysis, followed by molecular docking and molecular dynamic simulation studies to further explore the phytoconstituent's inhibitory mechanism of α-glucosidase, ∝-amylase, radical scavenging, and bacterial activity. The electronic structure and possible pharmacological actions of the phytocompound were revealed through the use of Density Functional Theory (DFT) analysis. Computational and in vitro studies revealed that these identified compounds have anti-diabetic, anti-oxidant, and anti-bacterial activities against antibiotic-resistant strain of Staphylococcus aureus.
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Affiliation(s)
- Nachammai Kathiresan
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India
| | - Kasilingam Harini
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India
| | - Arumugam Veera Ravi
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India
| | | | - Sangavi Pandi
- Department of Bioinformatics, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India
| | - Manikandan Ramesh
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India
| | - Collince Omondi Awere
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India
| | - Kulanthaivel Langeswaran
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India; Department of Biomedical Science, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India.
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91
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Kim T, Lee Y, Lim H, Kim Y, Cho H, Namkung W, Han G. Discovery of Protease-activated receptor 2 antagonists derived from phenylalanine for the treatment of breast cancer. Bioorg Chem 2024; 150:107496. [PMID: 38850590 DOI: 10.1016/j.bioorg.2024.107496] [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: 03/28/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/10/2024]
Abstract
Protease-activated receptor 2 (PAR2) has garnered attention as a potential therapeutic target in breast cancer. PAR2 is implicated in the activation of extracellular signal-regulated kinase 1/2 (ERK 1/2) via G protein and beta-arrestin pathways, contributing to the proliferation and metastasis of breast cancer cells. Despite the recognized role of PAR2 in breast cancer progression, clinically effective PAR2 antagonists remain elusive. To address this unmet clinical need, we synthesized and evaluated a series of novel compounds that target the orthosteric site of PAR2. Using in silico docking simulations, we identified compound 9a, an optimized derivative of compound 1a ((S)-N-(1-(benzylamino)-1-oxo-3-phenylpropan-2-yl)benzamide), which exhibited enhanced PAR2 antagonistic activity. Subsequent molecular dynamics simulations comparing 9a with the partial agonist 9d revealed that variations in ligand-induced conformational changes and interactions dictated whether the compound acted as an antagonist or agonist of PAR2. The results of this study suggest that further development of 9a could contribute to the advancement of PAR2 antagonists as potential therapeutic agents for breast cancer.
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Affiliation(s)
- Taegun Kim
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Yechan Lee
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Hocheol Lim
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Yeonhwa Kim
- Graduate Program of Industrial Pharmaceutical Science, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Haeun Cho
- Graduate Program of Industrial Pharmaceutical Science, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Wan Namkung
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Gyoonhee Han
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea; Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea.
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92
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Bhutkar M, Saha A, Tomar S. Viral methyltransferase inhibitors: berbamine, venetoclax, and ponatinib as efficacious antivirals against chikungunya virus. Arch Biochem Biophys 2024; 759:110111. [PMID: 39111614 DOI: 10.1016/j.abb.2024.110111] [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: 05/19/2024] [Revised: 07/20/2024] [Accepted: 08/03/2024] [Indexed: 08/13/2024]
Abstract
Chikungunya virus (CHIKV), transmitted by mosquitoes, poses a significant global health threat. Presently, no effective treatment options are available to reduce the disease burden. The lack of approved therapeutics against CHIKV and the complex spectrum of chronic musculoskeletal and neurological manifestations raise significant concerns, and repurposing drugs could offer swift avenues in the development of effective treatment strategies. RNA capping is a crucial step meditated by non-structural protein 1 (nsP1) in CHIKV replication. In this study, FDA-approved antivirals targeting CHIKV nsP1 methyltransferase (MTase) have been identified by structure-based virtual screening. Berbamine Hydrochloride (BH), ABT199/Venetoclax (ABT), and Ponatinib (PT) were the top-hits, which exhibited robust binding energies. Tryptophan fluorescence spectroscopy-based assay confirmed binding of BH-, ABT-, and PT to purified nsP1 with KD values ∼5.45 μM, ∼161.3 μM, and ∼3.83 μM, respectively. In a capillary electrophoresis-based assay, a decrease in CHIKV nsP1 MTase activity was observed in a dose-dependent manner. Treatment with BH, ABT, and PT lead to a dose-dependent reduction in the virus titer with IC50 < 100, ∼6.75, and <3.9 nM, respectively, and reduced viral mRNA levels. The nsP1 MTases are highly conserved among alphaviruses; therefore, BH, ABT, and PT, as expected, inhibited replication machinery in Sindbis virus (SINV) replicon assay with IC50 ∼1.94, ∼0.23, and >1.25 μM, respectively. These results highlight the potential of repurposing drugs as rapid and effective antiviral therapeutics against CHIKV.
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Affiliation(s)
- Mandar Bhutkar
- Molecular Virology Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Ankita Saha
- Molecular Virology Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Shailly Tomar
- Molecular Virology Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India.
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93
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Al-Madhagi H, Muhammed MT. Targeting COVID-19 and varicocele by blocking inflammasome: Ligand-based virtual screening. Arch Biochem Biophys 2024; 759:110107. [PMID: 39074718 DOI: 10.1016/j.abb.2024.110107] [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: 05/12/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 07/31/2024]
Abstract
COVID-19 is a new generation of outbreaks that invade not only local emerging region, continental but also the whole globe. Varicocele on the other hand, is a testicular vascular disease that underlies 40 % of male infertility cases. Fortunately, the two diseases can be blocked through targeting one common target, NLRP3 inflammasome. Upon searching for similar drugs that gained FDA-approval in ChEMBL library along with examining their potential blockade of the receptor through docking using CB-DOCK-2, three potential approved drugs can be repurposed, ChEMBL 4297185, ChEMBL 1201749, ChEMBL 1200545 which had binding energy of -9.8 and -9.7 kcal/mol (stronger than the reference inhibitor, -9.3 kcal/mol). Also, ADME profile of the top 3 drugs showed better attributes. Also, the simulated proteins exhibited stable pattern with strong free binding energies. Among the potential inhibitor drugs ChEMBL 4297185 was found to remain inside the binding site of the protein during the 200 ns simulation time. Hence, it is anticipated to have the highest binding and thus inhibition potential against the protein. The suggested drugs, especially ChEMBL 4297185, are potentially repurposable toward treating COVID-19 and varicocele which deserve further experimental validation.
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Affiliation(s)
| | - Muhammed Tilahun Muhammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Suleyman Demirel University, Isparta, Turkiye.
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94
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Escrich A, Jonguitud-Borrego N, Malcı K, Sanchez-Muñoz R, Palazon J, Rios-Solis L, Moyano E. A novel step towards the heterologous biosynthesis of paclitaxel: Characterization of T1βOH taxane hydroxylase. Metab Eng 2024; 85:201-212. [PMID: 39197725 DOI: 10.1016/j.ymben.2024.08.005] [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: 03/27/2024] [Revised: 06/25/2024] [Accepted: 08/21/2024] [Indexed: 09/01/2024]
Abstract
In the quest for innovative cancer therapeutics, paclitaxel remains a cornerstone in clinical oncology. However, its complex biosynthetic pathway, particularly the intricate oxygenation steps, has remained a puzzle in the decades following the characterization of the last taxane hydroxylase. The high divergence and promiscuity of enzymes involved have posed significant challenges. In this study, we adopted an innovative approach, combining in silico methods and functional gene analysis, to shed light on this elusive pathway. Our molecular docking investigations using a library of potential ligands uncovered TB574 as a potential missing enzyme in the paclitaxel biosynthetic pathway, demonstrating auspicious interactions. Complementary in vivo assays utilizing engineered S. cerevisiae strains as novel microbial cell factory consortia not only validated TB574's critical role in forging the elusive paclitaxel intermediate, T5αAc-1β,10β-diol, but also achieved the biosynthesis of paclitaxel precursors at an unprecedented yield including T5αAc-1β,10β-diol with approximately 40 mg/L. This achievement is highly promising, offering a new direction for further exploration of a novel metabolic engineering approaches using microbial consortia. In conclusion, our study not only furthers study the roles of previously uncharacterized enzymes in paclitaxel biosynthesis but also forges a path for pioneering advancements in the complete understanding of paclitaxel biosynthesis and its heterologous production. The characterization of T1βOH underscores a significant leap forward for future advancements in paclitaxel production using heterologous systems to improve cancer treatment and pharmaceutical production, thereby holding immense promise for enhancing the efficacy of cancer therapies and the efficiency of pharmaceutical manufacturing.
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Affiliation(s)
- Ainoa Escrich
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nestor Jonguitud-Borrego
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Koray Malcı
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - Raul Sanchez-Muñoz
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Javier Palazon
- Department of Biology, Healthcare and the Environment, Faculty of Pharmacy and Food Science, Universitat de Barcelona, Barcelona, Spain
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom; Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, London, WC1E 6EB, United Kingdom.
| | - Elisabeth Moyano
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
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95
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Han M, Kakar M, Li W, Iqbal I, Hu X, Liu Y, Tang Q, Sun L, Shakir Y, Liu T. Targeting MDM2-p53 interaction in Glioblastoma: Transcriptomic analysis and Peptide-Based inhibition strategy. Bioorg Chem 2024; 150:107620. [PMID: 38991490 DOI: 10.1016/j.bioorg.2024.107620] [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: 05/13/2024] [Revised: 06/26/2024] [Accepted: 07/07/2024] [Indexed: 07/13/2024]
Abstract
MDM2 is a gene that encodes a protein involved in cell survival, growth, and DNA repair. It has been implicated in the development and progression of glioblastoma (GBM). Inhibition of the MDM2-p53 interaction has emerged as a promising strategy for treating GBM. In this study, we performed comprehensive transcriptomic expression analysis from diverse datasets and observed MDM2 overexpression in a subset of GBM cases. MDM2 negatively regulates the major onco-suppressor p53. The interaction between MDM2 and p53 is a promising target for cancer therapy, as it can trigger p53-mediated cell death in response to different stress conditions, such as oncogene activation or DNA damage. In this study, we have identified a peptide-based inhibition of MDM2 as a therapeutic strategy for GBM. We have further validated the stability of the MDM2-peptide interaction using a molecular structural dynamics approach. The major trajectories, including root mean square of deviation (RMSD), root mean square of fluctuation (RMSF), and radius of gyration (RoG), indicate that the candidate peptides have a more stable binding compared to the native ligand and control drug. The stability of the binding interaction was further estimated by MMGBSA analysis, which also suggests that MDM2 has a stable binding with both peptide molecules. Based on these results, peptides P-1843 and P-3837 could be tested further for experimental validation to confirm their targeted inhibition of MDM-2. This approach could provide a highly selective and efficient inhibitor with potentially fewer side effects and less toxicity compared to small drug-based molecules.
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Affiliation(s)
- Manman Han
- Department of General Surgery, Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine, Zhejiang Province, China
| | - Mohibullah Kakar
- Faculty of Marine Sciences, Lasbela University of Agriculture, Water and Marine Sciences (LUAWMS), Uthal, Balochistan, Pakistan
| | - Wei Li
- Department of Oncology, The Affiliated Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province, China
| | - Imran Iqbal
- Department of PLR, Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany
| | - Xiaolin Hu
- Department of Oncology, The Affiliated Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province, China
| | - Yiting Liu
- Department of Oncology, The Affiliated Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province, China
| | - Qing Tang
- Department of Oncology, The Affiliated Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province, China
| | - Lizhu Sun
- Department of Oncology, The Affiliated Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province, China
| | - Yasmeen Shakir
- Department of Biochemistry, Hazara University, Mansehra, KPK, Pakistan.
| | - Tiantian Liu
- Department of Oncology, The Affiliated Shuyang Hospital of Xuzhou Medical University, Suqian City, Jiangsu Province, China.
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96
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Kong L, Park SJ, Im W. CHARMM-GUI PDB Reader and Manipulator: Covalent Ligand Modeling and Simulation. J Mol Biol 2024; 436:168554. [PMID: 39237201 PMCID: PMC11377865 DOI: 10.1016/j.jmb.2024.168554] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 09/07/2024]
Abstract
Molecular modeling and simulation serve an important role in exploring biological functions of proteins at the molecular level, which is complementary to experiments. CHARMM-GUI (https://www.charmm-gui.org) is a web-based graphical user interface that generates complex molecular simulation systems and input files, and we have been continuously developing and expanding its functionalities to facilitate various complex molecular modeling and make molecular dynamics simulations more accessible to the scientific community. Currently, covalent drug discovery emerges as a popular and important field. Covalent drug forms a chemical bond with specific residues on the target protein, and it has advantages in potency for its prolonged inhibition effects. Even though there are higher demands in modeling PDB protein structures with various covalent ligand types, proper modeling of covalent ligands remains challenging. This work presents a new functionality in CHARMM-GUI PDB Reader & Manipulator that can handle a diversity of ligand-amino acid linkage types, which is validated by a careful benchmark study using over 1,000 covalent ligand structures in RCSB PDB. We hope that this new functionality can boost the modeling and simulation study of covalent ligands.
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Affiliation(s)
- Lingyang Kong
- Departments of Biological Sciences, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Sang-Jun Park
- Departments of Biological Sciences, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Wonpil Im
- Departments of Biological Sciences, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA.
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97
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Yousaf MA, Basheera S, Sivanandan S. Inhibition of Monkeypox Virus DNA Polymerase Using Moringa oleifera Phytochemicals: Computational Studies of Drug-Likeness, Molecular Docking, Molecular Dynamics Simulation and Density Functional Theory. Indian J Microbiol 2024; 64:1057-1074. [PMID: 39282169 PMCID: PMC11399536 DOI: 10.1007/s12088-024-01244-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/28/2024] [Indexed: 09/18/2024] Open
Abstract
The emergence of zoonotic monkeypox (MPX) disease, caused by the double-stranded DNA monkeypox virus (MPXV), has become a global threat. Due to unavailability of a specific small molecule drug for MPX, this study investigated Moringa oleifera phytochemicals to find potent and safe inhibitors of DNA Polymerase (DNA Pol), a poxvirus drug target due to its role in the viral life cycle. For that, 146 phytochemicals were screened through drug-likeness and molecular docking analyses. Among these, 136 compounds exhibited drug-like properties, with Gossypetin showing the highest binding affinity (- 7.8 kcal/mol), followed by Riboflavin (- 7.6 kcal/mol) and Ellagic acid (- 7.6 kcal/mol). In comparison, the control drugs Cidofovir and Brincidofovir displayed lower binding affinities, with binding energies of - 6.0 kcal/mol and - 5.1 kcal/mol, respectively. Hydrogen bonds, electrostatic and hydrophobic interactions were the main non-bond interactions between inhibitors and protein active site. The identified compounds were further evaluated using molecular dynamics simulation, density functional theory analysis and ADMET analysis. Molecular dynamics simulations conducted over 200 ns revealed that DNA Pol-Gossypetin complex was not stable, however, Riboflavin and Ellagic acid complexes showed excellent stability indicating them as better DNA Pol inhibitors. The density functional theory analysis exhibited the chemical reactivity of these inhibitor compounds. The ADMET analysis suggested that the top phytochemicals were safe and showed no toxicity. In conclusion, this study has identified Riboflavin and Ellagic acid as potential DNA Pol inhibitors to control MPXV. Further experimental assays and clinical trials are needed to confirm their activity against the disease. Graphical Abstract
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Affiliation(s)
- Muhammad Abrar Yousaf
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Shefin Basheera
- Department of Biotechnology and Bioinformatics, Saraswathy Thangavelu Extension Centre, A Research Centre of University of Kerala, KSCSTE-Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, India
| | - Sreekumar Sivanandan
- Department of Biotechnology and Bioinformatics, Saraswathy Thangavelu Extension Centre, A Research Centre of University of Kerala, KSCSTE-Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, India
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98
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Harms M, Haase A, Rodríguez-Alfonso A, Löffler J, Almeida-Hernández Y, Ruiz-Blanco YB, Albers D, Gilg A, von Bank F, Zech F, Groß R, Datta M, Jaikishan J, Draphoen B, Habib M, Ständker L, Wiese S, Lindén M, Winter G, Rasche V, Beer AJ, Jumaa H, Abadi AH, Kirchhoff F, Busch M, Dünker N, Sanchez-Garcia E, Münch J. Fatty acid conjugated EPI-X4 derivatives with increased activity and in vivo stability. J Control Release 2024; 373:583-598. [PMID: 39047872 DOI: 10.1016/j.jconrel.2024.07.049] [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: 03/19/2024] [Revised: 07/09/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
Dysregulation of the CXCL12/CXCR4 axis is implicated in autoimmune, inflammatory, and oncogenic diseases, positioning CXCR4 as a pivotal therapeutic target. We evaluated optimized variants of the specific endogenous CXCR4 antagonist, EPI-X4, addressing existing challenges in stability and potency. Our structure-activity relationship study investigates the conjugation of EPI-X4 derivatives with long-chain fatty acids, enhancing serum albumin interaction and receptor affinity. Molecular dynamic simulations revealed that the lipid moieties stabilize the peptide-receptor interaction through hydrophobic contacts at the receptor's N-terminus, anchoring the lipopeptide within the CXCR4 binding pocket and maintaining essential receptor interactions. Accordingly, lipidation resulted in increased receptor affinities and antagonistic activities. Additionally, by interacting with human serum albumin lipidated EPI-X4 derivatives displayed sustained stability in human plasma and extended circulation times in vivo. Selected candidates showed significant therapeutic potential in human retinoblastoma cells in vitro and in ovo, with our lead derivative exhibiting higher efficacies compared to its non-lipidated counterpart. This study not only elucidates the optimization trajectory for EPI-X4 derivatives but also underscores the intricate interplay between stability and efficacy, crucial for delineating their translational potential in clinical applications.
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Affiliation(s)
- Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.
| | - André Haase
- Institute for Anatomy II, Department of Neuroanatomy, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany
| | - Armando Rodríguez-Alfonso
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm 89081, Germany; Core Unit Mass Spectrometry and Proteomics, Ulm University Medical Center, Ulm 89081, Germany
| | - Jessica Löffler
- Department of Nuclear Medicine, Ulm University Medical Center, Ulm 89081, Germany
| | - Yasser Almeida-Hernández
- Computational Bioengineering, Department of Biochemical and Chemical Engineering, 44227 Dortmund, Germany
| | - Yasser B Ruiz-Blanco
- Computational Bioengineering, Department of Biochemical and Chemical Engineering, 44227 Dortmund, Germany
| | - Dan Albers
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Andrea Gilg
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Franziska von Bank
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Moumita Datta
- Institute of Immunology, Ulm University Medical Center, Ulm 89081, Germany
| | - Janeni Jaikishan
- Institute of Immunology, Ulm University Medical Center, Ulm 89081, Germany
| | | | - Monica Habib
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt; Pharmaceutical Chemistry Department, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, Cairo, Egypt
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm 89081, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University Medical Center, Ulm 89081, Germany
| | - Mika Lindén
- Institute for Inorganic Chemistry II, 89081 Ulm, Germany
| | - Gordon Winter
- Department of Nuclear Medicine, Ulm University Medical Center, Ulm 89081, Germany
| | - Volker Rasche
- Experimental Cardiovascular Imaging (ExCaVI), Ulm University Medical Center, Ulm 89081, Germany
| | - Ambros J Beer
- Department of Nuclear Medicine, Ulm University Medical Center, Ulm 89081, Germany
| | - Hassan Jumaa
- Institute of Immunology, Ulm University Medical Center, Ulm 89081, Germany
| | - Ashraf H Abadi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Maike Busch
- Institute for Anatomy II, Department of Neuroanatomy, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany
| | - Nicole Dünker
- Institute for Anatomy II, Department of Neuroanatomy, Center for Translational Neuro- and Behavioral Sciences (C-TNBS), Medical Faculty, University of Duisburg-Essen, 45147 Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Bioengineering, Department of Biochemical and Chemical Engineering, 44227 Dortmund, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
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99
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Ho TH, Hien TD, Wilhelmsen Ø, Trinh TT. Thermophysical properties of polyethylene glycol oligomers via molecular dynamics simulations. RSC Adv 2024; 14:28125-28137. [PMID: 39228756 PMCID: PMC11369976 DOI: 10.1039/d4ra04898a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Accepted: 08/24/2024] [Indexed: 09/05/2024] Open
Abstract
Polyethylene glycol (PEG) is a versatile chemical with numerous applications in various fields, including biomedical research, pharmaceutical development, and industrial manufacturing. Molecular dynamics (MD) is a powerful tool for investigating the thermophysical properties of PEG molecules. In this study, we employ the General AMBER force field (GAFF) to perform MD simulations on various PEG oligomers, focusing on the calculation of density, self-diffusion coefficients, shear viscosity, and thermal conductivity. The results demonstrate excellent agreement with experimental data, where GAFF outperforms other force fields in reproducing thermophysical properties. For a PEG tetramer, the GAFF force field reproduces experimental data within 5% for the density, 5% for the diffusion coefficient, and 10% for the viscosity. In comparison, the OPLS force field displays significant deviations exceeding 80% for the diffusion coefficient and 400% for the viscosity. A detailed analysis of partial charge distributions and dihedral angles reveals that they significantly impact the structural behavior of PEG oligomers. The findings highlight the GAFF force field as one of the most accurate and reliable options for simulating systems with PEGs.
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Affiliation(s)
- Thi H Ho
- Laboratory for Computational Physics, Institute for Computational Science and Artificial Intelligence, Van Lang University Ho Chi Minh City Vietnam
- Faculty of Mechanical - Electrical and Computer Engineering, School of Technology, Van Lang University Ho Chi Minh City Vietnam
| | - Tong Duy Hien
- Faculty of Engineering, Vietnamese-German University (VGU) Thu Dau Mot City Binh Duong Province 75000 Vietnam
| | - Øivind Wilhelmsen
- Department of Chemistry, Porelab, Norwegian University of Science and Technology Trondheim Norway
| | - Thuat T Trinh
- Department of Chemistry, Porelab, Norwegian University of Science and Technology Trondheim Norway
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Jin Y, Perez-Lemus GR, Zubieta Rico PF, de Pablo JJ. Improving Machine Learned Force Fields for Complex Fluids through Enhanced Sampling: A Liquid Crystal Case Study. J Phys Chem A 2024; 128:7257-7268. [PMID: 39150905 DOI: 10.1021/acs.jpca.4c01546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2024]
Abstract
Machine learned force fields offer the potential for faster execution times while retaining the accuracy of traditional DFT calculations, making them promising candidates for molecular simulations in cases where reliable classical force fields are not available. Some of the challenges associated with machine learned force fields include simulation stability over extended periods of time and ensuring that the statistical and dynamical properties of the underlying simulated systems are correctly captured. In this work, we propose a systematic training pipeline for such force fields that leads to improved model quality, compared to that achieved by traditional data generation and training approaches. That pipeline relies on the use of enhanced sampling techniques, and it is demonstrated here in the context of a liquid crystal, which exemplifies many of the challenges that are encountered in fluids and materials with complex free energy landscapes. Our results indicate that, whereas the majority of traditional machine learned force field training approaches lead to molecular dynamics simulations that are only stable over hundred-picosecond trajectories, our approach allows for stable simulations over tens of nanoseconds for organic molecular systems comprising thousands of atoms.
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Affiliation(s)
- Yezhi Jin
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637-1476, United States
| | - Gustavo R Perez-Lemus
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637-1476, United States
| | - Pablo F Zubieta Rico
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637-1476, United States
| | - Juan J de Pablo
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637-1476, United States
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