1
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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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2
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Simon JP, Dong S. In-silico screening of missense nsSNPs in Delta-opioid receptor protein and their restoring tendency on MCRT interaction; focusing on dynamic nature. Int J Biol Macromol 2024; 275:133710. [PMID: 38977046 DOI: 10.1016/j.ijbiomac.2024.133710] [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: 04/29/2024] [Revised: 06/30/2024] [Accepted: 07/05/2024] [Indexed: 07/10/2024]
Abstract
Delta-opioid receptor protein (OPRD1) is one of the potential targets for treating pain. The presently available opioid agonists are known to cause unnecessary side effects. To discover a novel opioid agonist, our research group has synthesized a chimeric peptide MCRT and proved its potential activity through in vivo analysis. Non-synonymous SNPs (nsSNPs) missense mutations affect the functionality and stability of proteins leading to diseases. The current research was focused on understanding the role of MCRT in restoring the binding tendency of OPRD1 nsSNPs missense mutations on dynamic nature in comparison with Deltorphin-II and morphiceptin. The deleterious effects of nsSNPs were analyzed using various bioinformatics tools for predicting structural, functional, and oncogenic influence. The shortlisted nine nsSNPs were predicted for allergic reactions, domain changes, post-translation modification, multiple sequence alignment, secondary structure, molecular dynamic simulation (MDS), and peptide docking influence. Further, the docked complex of three shortlisted deleterious nsSNPs was analyzed using an MDS study, and the highly deleterious shortlisted nsSNP A149T was further analyzed for higher trajectory analysis. MCRT restored the binding tendency influence caused by nsSNPs on the dynamics of stability, functionality, binding affinity, secondary structure, residues connection, motion, and folding of OPRD1 protein.
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Affiliation(s)
- Jerine Peter Simon
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China
| | - Shouliang Dong
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China,; Key Laboratory of Preclinical Study for New Drugs of Gansu Province, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China.
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3
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Waterhouse AM, Studer G, Robin X, Bienert S, Tauriello G, Schwede T. The structure assessment web server: for proteins, complexes and more. Nucleic Acids Res 2024; 52:W318-W323. [PMID: 38634802 PMCID: PMC11223858 DOI: 10.1093/nar/gkae270] [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: 02/02/2024] [Revised: 03/21/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
The 'structure assessment' web server is a one-stop shop for interactive evaluation and benchmarking of structural models of macromolecular complexes including proteins and nucleic acids. A user-friendly web dashboard links sequence with structure information and results from a variety of state-of-the-art tools, which facilitates the visual exploration and evaluation of structure models. The dashboard integrates stereochemistry information, secondary structure information, global and local model quality assessment of the tertiary structure of comparative protein models, as well as prediction of membrane location. In addition, a benchmarking mode is available where a model can be compared to a reference structure, providing easy access to scores that have been used in recent CASP experiments and CAMEO. The structure assessment web server is available at https://swissmodel.expasy.org/assess.
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Affiliation(s)
- Andrew M Waterhouse
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Gabriel Studer
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Xavier Robin
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Stefan Bienert
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Gerardo Tauriello
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
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4
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Bugnon M, Röhrig UF, Goullieux M, Perez MS, Daina A, Michielin O, Zoete V. SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina. Nucleic Acids Res 2024; 52:W324-W332. [PMID: 38686803 PMCID: PMC11223881 DOI: 10.1093/nar/gkae300] [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: 01/31/2024] [Revised: 03/19/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024] Open
Abstract
Drug discovery aims to identify potential therapeutic compounds capable of modulating the activity of specific biological targets. Molecular docking can efficiently support this process by predicting binding interactions between small molecules and macromolecular targets and potentially accelerating screening campaigns. SwissDock is a computational tool released in 2011 as part of the SwissDrugDesign project, providing a free web-based service for small-molecule docking after automatized preparation of ligands and targets. Here, we present the latest version of SwissDock, in which EADock DSS has been replaced by two state-of-the-art docking programs, i.e. Attracting Cavities and AutoDock Vina. AutoDock Vina provides faster docking predictions, while Attracting Cavities offers more accurate results. Ligands can be imported in various ways, including as files, SMILES notation or molecular sketches. Targets can be imported as PDB files or identified by their PDB ID. In addition, advanced search options are available both for ligands and targets, giving users automatized access to widely-used databases. The web interface has been completely redesigned for interactive submission and analysis of docking results. Moreover, we developed a user-friendly command-line access which, in addition to all options of the web site, also enables covalent ligand docking with Attracting Cavities. The new version of SwissDock is freely available at https://www.swissdock.ch/.
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Affiliation(s)
- Marine Bugnon
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Ute F Röhrig
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Mathilde Goullieux
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Marta A S Perez
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Antoine Daina
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Olivier Michielin
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
- Department of Oncology, Geneva University Hospital (HUG), CH-1205 Geneva, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
- Department of Oncology UNIL-CHUV, Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne, CH-1015 Lausanne, Switzerland
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5
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Monticelli M, Hay Mele B, Wright DM, Guerriero S, Andreotti G, Cubellis MV. Exploring ligand interactions with human phosphomannomutases using recombinant bacterial thermal shift assay and biochemical validation. Biochimie 2024; 222:123-131. [PMID: 38458414 DOI: 10.1016/j.biochi.2024.02.011] [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: 02/02/2024] [Accepted: 02/26/2024] [Indexed: 03/10/2024]
Abstract
PMM2-CDG, a disease caused by mutations in phosphomannomutase-2, is the most common congenital disorder of glycosylation. Yet, it still lacks a cure. Targeting phosphomannomutase-2 with pharmacological chaperones or inhibiting the phosphatase activity of phosphomannomutase-1 to enhance intracellular glucose-1,6-bisphosphate have been proposed as therapeutical approaches. We used Recombinant Bacterial Thermal Shift Assay to assess the binding of a substrate analog to phosphomannomutase-2 and the specific binding to phosphomannomutase-1 of an FDA-approved drug - clodronate. We also deepened the clodronate binding by enzyme activity assays and in silico docking. Our results confirmed the selective binding of clodronate to phosphomannomutase-1 and shed light on such binding.
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Affiliation(s)
- Maria Monticelli
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy; Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy
| | - Bruno Hay Mele
- Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy
| | - Demi Marie Wright
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy; Institute of Chemistry and Biochemistry, Freie Universität Berlin, D-14195, Berlin, Germany
| | - Simone Guerriero
- Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy
| | - Giuseppina Andreotti
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy.
| | - Maria Vittoria Cubellis
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy; Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy; Stazione Zoologica "Anton Dohrn", Villa Comunale, Naples, Italy
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6
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Mareuil F, Moine-Franel A, Kar A, Nilges M, Ciambur CB, Sperandio O. Protein interaction explorer (PIE): a comprehensive platform for navigating protein-protein interactions and ligand binding pockets. Bioinformatics 2024; 40:btae414. [PMID: 38917415 PMCID: PMC11223782 DOI: 10.1093/bioinformatics/btae414] [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: 01/16/2024] [Revised: 06/12/2024] [Accepted: 06/24/2024] [Indexed: 06/27/2024] Open
Abstract
SUMMARY Protein Interaction Explorer (PIE) is a new web-based tool integrated to our database iPPI-DB, specifically crafted to support structure-based drug discovery initiatives focused on protein-protein interactions (PPIs). Drawing upon extensive structural data encompassing thousands of heterodimer complexes, including those with successful ligands, PIE provides a comprehensive suite of tools dedicated to aid decision-making in PPI drug discovery. PIE enables researchers/bioinformaticians to identify and characterize crucial factors such as the presence of binding pockets or functional binding sites at the interface, predicting hot spots, and foreseeing similar protein-embedded pockets for potential repurposing efforts. AVAILABILITY AND IMPLEMENTATION PIE is user-friendly and readily accessible at https://ippidb.pasteur.fr/targetcentric/. It relies on the NGL visualizer.
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Affiliation(s)
- Fabien Mareuil
- Bioinformatics and Biostatistics Hub, Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 75015 Paris, France
| | - Alexandra Moine-Franel
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, Université de Paris, CNRS UMR3528, 75015 Paris, France
- Collège Doctoral, Sorbonne Université, 75005 Paris, France
| | - Anuradha Kar
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, Université de Paris, CNRS UMR3528, 75015 Paris, France
| | - Michael Nilges
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, Université de Paris, CNRS UMR3528, 75015 Paris, France
| | - Constantin Bogdan Ciambur
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, Université de Paris, CNRS UMR3528, 75015 Paris, France
| | - Olivier Sperandio
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, Université de Paris, CNRS UMR3528, 75015 Paris, France
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7
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Zhang W, Guan H, Wang M, Wang W, Pu J, Zou H, Li D. Exploring the Relationship between Small Peptides and the T1R1/T1R3 Umami Taste Receptor for Umami Peptide Prediction: A Combined Approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:13262-13272. [PMID: 38775286 DOI: 10.1021/acs.jafc.4c00187] [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: 05/31/2024]
Abstract
Umami peptides are known for enhancing the taste experience by binding to oral umami T1R1 and T1R3 receptors. Among them, small peptides (composed of 2-4 amino acids) constitute nearly 40% of reported umami peptides. Given the diversity in amino acids and peptide sequences, umami small peptides possess tremendous untapped potential. By investigating 168,400 small peptides, we screened candidates binding to T1R1/T1R3 through molecular docking and molecular dynamics simulations, explored bonding types, amino acid characteristics, preferred binding sites, etc. Utilizing three-dimensional molecular descriptors, bonding information, and a back-propagation neural network, we developed a predictive model with 90.3% accuracy, identifying 24,539 potential umami peptides. Clustering revealed three classes with distinct logP (-2.66 ± 1.02, -3.52 ± 0.93, -2.44 ± 1.23) and asphericity (0.28 ± 0.12, 0.26 ± 0.11, 0.25 ± 0.11), indicating significant differences in shape and hydrophobicity (P < 0.05) among potential umami peptides binding to T1R1/T1R3. Following clustering, nine representative peptides (CQ, DP, NN, CSQ, DMC, TGS, DATE, HANR, and STAN) were synthesized and confirmed to possess umami taste through sensory evaluations and electronic tongue analyses. In summary, this study provides insights into exploring small peptide interactions with umami receptors, advancing umami peptide prediction models.
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Affiliation(s)
- Wenyuan Zhang
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian 271018, People's Republic of China
| | - Hui Guan
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian 271018, People's Republic of China
| | - Miaomiao Wang
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian 271018, People's Republic of China
| | - Wenyu Wang
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian 271018, People's Republic of China
| | - Jianyu Pu
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian 271018, People's Republic of China
| | - Hui Zou
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian 271018, People's Republic of China
| | - Dapeng Li
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Nutrition and Human Health in Universities of Shandong, Taian 271018, People's Republic of China
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8
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Mei C, Zhang J, Niu Z, Simon JP, Yang T, Huang M, Zhang Z, Zhou L, Dong S. MP-13, a novel chimeric peptide of morphiceptin and pepcan-9, produces potent antinociception with limited side effects. Neuropeptides 2024; 107:102440. [PMID: 38875739 DOI: 10.1016/j.npep.2024.102440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024]
Abstract
Pharmacological investigations have substantiated the potential of bifunctional opioid/cannabinoid agonists in delivering potent analgesia while minimizing adverse reactions. Peptide modulators of cannabinoid receptors, known as pepcans, have been investigated before. In this study, we designed a series of chimeric peptides based on pepcans and morphiceptin (YPFP-NH2). Here, we combined injections of pepcans and morphiceptin to investigate the combination treatment of opioids and cannabis and compared the analgesic effect with chimeric compounds. Subsequently, we employed computational docking to screen the compounds against opioid and cannabinoid receptors, along with an acute pain model, to identify the most promising peptide. Among these peptides, MP-13, a morphiceptin and pepcan-9 (PVNFKLLSH) construct, exhibited superior supraspinal analgesic efficacy in the tail-flick test, with an ED50 value at 1.43 nmol/mouse, outperforming its parent peptides and other chimeric analogs. Additionally, MP-13 displayed potent analgesic activity mediated by mu-opioid receptor (MOR), delta-opioid receptor (DOR), and cannabinoid type 1 (CB1) receptor pathways. Furthermore, MP-13 did not induce psychological dependence and gastrointestinal motility inhibition at the effective analgesic doses, and it maintained non-tolerance-forming antinociception throughout a 7-day treatment regimen, with an unaltered count of microglial cells in the periaqueductal gray region, supporting this observation. Moreover, intracerebroventricular administration of MP-13 demonstrated dose-dependent antinociception in murine models of neuropathic, inflammatory, and visceral pain. Our findings provide promising insights for the development of opioid/cannabinoid peptide agonists, addressing a crucial gap in the field and holding significant potential for future research and development. PERSPECTIVE: This article offers insights into the combination treatment of pepcans with morphiceptin. Among the chimeric peptides, MP-13 exhibited potent analgesic effects in a series of preclinical pain models with a favorable side-effect profile.
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Affiliation(s)
- Chenxi Mei
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China
| | - Jing Zhang
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China
| | - Zhanyu Niu
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China
| | - Jerine Peter Simon
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China
| | - Tong Yang
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China
| | - Mingmin Huang
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China
| | - Zhonghua Zhang
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China
| | - Lanxia Zhou
- Laboratory of Clinical Molecular Cytogenetics and Immunology, the First Hospital, Lanzhou University, 1 Donggang West Road, Lanzhou 730000, China
| | - Shouliang Dong
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China; Key Laboratory of Preclinical Study for New Drugs of Gansu Province, Lanzhou University, 222 Tianshui South Road, Lanzhou 730000, China.
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9
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Diedrich K, Ehrt C, Graef J, Poppinga M, Ritter N, Rarey M. User-centric design of a 3D search interface for protein-ligand complexes. J Comput Aided Mol Des 2024; 38:23. [PMID: 38814371 PMCID: PMC11139749 DOI: 10.1007/s10822-024-00563-3] [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: 04/03/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024]
Abstract
In this work, we present the frontend of GeoMine and showcase its application, focusing on the new features of its latest version. GeoMine is a search engine for ligand-bound and predicted empty binding sites in the Protein Data Bank. In addition to its basic text-based search functionalities, GeoMine offers a geometric query type for searching binding sites with a specific relative spatial arrangement of chemical features such as heavy atoms and intermolecular interactions. In contrast to a text search that requires simple and easy-to-formulate user input, a 3D input is more complex, and its specification can be challenging for users. GeoMine's new version aims to address this issue from the graphical user interface perspective by introducing an additional visualization concept and a new query template type. In its latest version, GeoMine extends its query-building capabilities primarily through input formulation in 2D. The 2D editor is fully synchronized with GeoMine's 3D editor and provides the same functionality. It enables template-free query generation and template-based query selection directly in 2D pose diagrams. In addition, the query generation with the 3D editor now supports predicted empty binding sites for AlphaFold structures as query templates. GeoMine is freely accessible on the ProteinsPlus web server ( https://proteins.plus ).
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Affiliation(s)
- Konrad Diedrich
- Universität Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany
| | - Christiane Ehrt
- Universität Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany
| | - Joel Graef
- Universität Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany
| | - Martin Poppinga
- Universität Hamburg, Department of Informatics, Vogt-Kölln-Straße 30, 22527, Hamburg, Germany
| | - Norbert Ritter
- Universität Hamburg, Department of Informatics, Vogt-Kölln-Straße 30, 22527, Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany.
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10
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Zhang W, Liu Y, Jang H, Nussinov R. CDK2 and CDK4: Cell Cycle Functions Evolve Distinct, Catalysis-Competent Conformations, Offering Drug Targets. JACS AU 2024; 4:1911-1927. [PMID: 38818077 PMCID: PMC11134382 DOI: 10.1021/jacsau.4c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/08/2024] [Accepted: 05/06/2024] [Indexed: 06/01/2024]
Abstract
Cyclin-dependent kinases (CDKs), particularly CDK4 and CDK2, are crucial for cell cycle progression from the Gap 1 (G1) to the Synthesis (S) phase by phosphorylating targets such as the Retinoblastoma Protein (Rb). CDK4, paired with cyclin-D, operates in the long G1 phase, while CDK2 with cyclin-E, manages the brief G1-to-S transition, enabling DNA replication. Aberrant CDK signaling leads to uncontrolled cell proliferation, which is a hallmark of cancer. Exactly how they accomplish their catalytic phosphorylation actions with distinct efficiencies poses the fundamental, albeit overlooked question. Here we combined available experimental data and modeling of the active complexes to establish their conformational functional landscapes to explain how the two cyclin/CDK complexes differentially populate their catalytically competent states for cell cycle progression. Our premise is that CDK catalytic efficiencies could be more important for cell cycle progression than the cyclin-CDK biochemical binding specificity and that efficiency is likely the prime determinant of cell cycle progression. We observe that CDK4 is more dynamic than CDK2 in the ATP binding site, the regulatory spine, and the interaction with its cyclin partner. The N-terminus of cyclin-D acts as an allosteric regulator of the activation loop and the ATP-binding site in CDK4. Integrated with a suite of experimental data, we suggest that the CDK4 complex is less capable of remaining in the active catalytically competent conformation, and may have a lower catalytic efficiency than CDK2, befitting their cell cycle time scales, and point to critical residues and motifs that drive their differences. Our mechanistic landscape may apply broadly to kinases, and we propose two drug design strategies: (i) allosteric Inhibition by conformational stabilization for targeting allosteric CDK4 regulation by cyclin-D, and (ii) dynamic entropy-optimized targeting which leverages the dynamic, entropic aspects of CDK4 to optimize drug binding efficacy.
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Affiliation(s)
- Wengang Zhang
- Cancer
Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Yonglan Liu
- Cancer
Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Hyunbum Jang
- Computational
Structural Biology Section, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ruth Nussinov
- Computational
Structural Biology Section, Frederick National
Laboratory for Cancer Research, Frederick, Maryland 21702, United States
- Department
of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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11
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Weber P, Bojarová P, Brouzdová J, Křen V, Kulik N, Stütz AE, Thonhofer M, Wrodnigg TM. Diaminocyclopentane - l-Lysine Adducts: Potent and selective inhibitors of human O-GlcNAcase. Bioorg Chem 2024; 148:107452. [PMID: 38763001 DOI: 10.1016/j.bioorg.2024.107452] [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: 04/18/2024] [Accepted: 05/11/2024] [Indexed: 05/21/2024]
Abstract
A new class of compounds, namely highly substituted diaminocyclopentane-l-lysine adducts, have been discovered as potent inhibitors of O-GlcNAcase, an enzyme crucial for protein de-O-glycosylation. These inhibitors exhibit exceptional selectivity and reversibility and are the first example of human O-GlcNAcase inhibitors that are structurally related to the transition state of the rate-limiting step with the "aglycon" still in bond-length proximity. The ease of their preparation, remarkable biological activities, stability, and non-toxicity make them promising candidates for the development of anti-tau-phosphorylation agents holding significant potential for the treatment of Alzheimer's disease.
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Affiliation(s)
- Patrick Weber
- Glycogroup, Institute of Chemistry and Technology of Biobased Systems, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria.
| | - Pavla Bojarová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic
| | - Jitka Brouzdová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic
| | - Vladimír Křen
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic
| | - Natalia Kulik
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14220 Prague 4, Czech Republic
| | - Arnold E Stütz
- Glycogroup, Institute of Chemistry and Technology of Biobased Systems, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria.
| | - Martin Thonhofer
- Glycogroup, Institute of Chemistry and Technology of Biobased Systems, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Tanja M Wrodnigg
- Glycogroup, Institute of Chemistry and Technology of Biobased Systems, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
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12
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Liu Y, Deng L, Ding F, Wang Q, Zhang S, Mi N, Zhang W, Zeng B, Tong H, Wu L. Discovery of novel cholesteryl ester transfer protein (CETP) inhibitors by a multi-stage virtual screening. BMC Chem 2024; 18:95. [PMID: 38702788 PMCID: PMC11069292 DOI: 10.1186/s13065-024-01192-5] [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: 02/03/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
Cholesteryl ester transfer protein (CETP) is a promising therapeutic target for cardiovascular diseases. It effectively lowers the low-density lipoprotein cholesterol levels and increases the high-density lipoprotein cholesterol levels in the human plasma. This study identified novel and highly potent CETP inhibitors using virtual screening techniques. Molecular docking and molecular dynamics (MD) simulations revealed the binding patterns of these inhibitors, with the top 50 compounds selected according to their predicted binding affinity. Protein-ligand interaction analyses were performed, leading to the selection of 26 compounds for further evaluation. A CETP inhibition assay confirmed the inhibitory activities of the selected compounds. The results of the MD simulations revealed the structural stability of the protein-ligand complexes, with the binding site remaining significantly unchanged, indicating that the five compounds (AK-968/40709303, AG-690/11820117, AO-081/41378586, AK-968/12713193, and AN-465/14952302) identified have the potential as active CETP inhibitors and are promising leads for drug development.
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Affiliation(s)
- Yanfeng Liu
- Nanjing Lishui District Hospital of Traditional Chinese Medicine, Nanjing, China
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Liangying Deng
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Feng Ding
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qiang Wang
- Nanjing Lishui District Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Shuran Zhang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Nana Mi
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Wenhui Zhang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Bailin Zeng
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Huangjin Tong
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Lixing Wu
- Nanjing Lishui District Hospital of Traditional Chinese Medicine, Nanjing, China.
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
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13
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Tang Z, Wang S, Du L, Hu D, Chen X, Zheng H, Ding H, Chen S, Zhang L, Zhang N. The impact of micropolymorphism in Anpl-UAA on structural stability and peptide presentation. Int J Biol Macromol 2024; 267:131665. [PMID: 38636758 DOI: 10.1016/j.ijbiomac.2024.131665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Micropolymorphism significantly shapes the peptide-binding characteristics of major histocompatibility complex class I (MHC-I) molecules, affecting the host's resistance to pathogens, which is particularly pronounced in avian species displaying the "minimal essential MHC" expression pattern. In this study, we compared two duck MHC-I alleles, Anpl-UAA*77 and Anpl-UAA*78, that exhibit markedly different peptide binding properties despite their high sequence homology. Through mutagenesis experiments and crystallographic analysis of complexes with the influenza virus-derived peptide AEAIIVAMV (AEV9), we identified a critical role for the residue at position 62 in regulating hydrogen-bonding interactions between the peptide backbone and the peptide-binding groove. This modulation affects the characteristics of the B pocket and the stability of the loop region between the 310 helix and the α1 helix, leading to significant changes in the structure and stability of the peptide-MHC-I complex (pMHC-I). Moreover, the proportion of different residues at position 62 among Anpl-UAAs may reflect the correlation between pAnpl-UAA stability and duck body temperature. This research not only advances our understanding of the Anpl-UAA structure but also deepens our insight into the impact of MHC-I micropolymorphism on peptide binding.
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Affiliation(s)
- Ziche Tang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Suqiu Wang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Liubao Du
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Dongmei Hu
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiaoming Chen
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hanyin Zheng
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Han Ding
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Shiwen Chen
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Lin Zhang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China; Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan 250100, Shandong, China.
| | - Nianzhi Zhang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China..
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14
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Yan X, Zhang X, Li H, Deng D, Guo Z, Kang L, Li A. Engineering of Unspecific Peroxygenases Using a Superfolder-Green-Fluorescent-Protein-Mediated Secretion System in Escherichia coli. JACS AU 2024; 4:1654-1663. [PMID: 38665664 PMCID: PMC11040664 DOI: 10.1021/jacsau.4c00129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024]
Abstract
Unspecific peroxygenases (UPOs), secreted by fungi, demonstrate versatility in catalyzing challenging selective oxyfunctionalizations. However, the number of peroxygenases and corresponding variants with tailored selectivity for a broader substrate scope is still limited due to the lack of efficient engineering strategies. In this study, a new unspecific peroxygenase from Coprinopsis marcescibilis (CmaUPO) is identified and characterized. To enhance or reverse the enantioselectivity of wildtype (WT) CmaUPO catalyzed asymmetric hydroxylation of ethylbenzene, CmaUPO was engineered using an efficient superfolder-green-fluorescent-protein (sfGFP)-mediated secretion system in Escherichia coli. Iterative saturation mutagenesis (ISM) was used to target the residual sites lining the substrate tunnel, resulting in two variants: T125A/A129G and T125A/A129V/A247H/T244A/F243G. The two variants greatly improved the enantioselectivities [21% ee (R) for WT], generating the (R)-1-phenylethanol or (S)-1-phenylethanol as the main product with 99% ee (R) and 84% ee (S), respectively. The sfGFP-mediated secretion system in E. coli demonstrates applicability for different UPOs (AaeUPO, CciUPO, and PabUPO-I). Therefore, this developed system provides a robust platform for heterologous expression and enzyme engineering of UPOs, indicating great potential for their sustainable and efficient applications in various chemical transformations.
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Affiliation(s)
| | | | | | - Di Deng
- State Key Laboratory of Biocatalysis
and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology,
School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
| | - Zhiyong Guo
- State Key Laboratory of Biocatalysis
and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology,
School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
| | - Lixin Kang
- State Key Laboratory of Biocatalysis
and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology,
School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
| | - Aitao Li
- State Key Laboratory of Biocatalysis
and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology,
School of Life Sciences, Hubei University, #368 Youyi Road, Wuhan 430062, P. R. China
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15
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Daoud S, Taha M. Protein characteristics substantially influence the propensity of activity cliffs among kinase inhibitors. Sci Rep 2024; 14:9058. [PMID: 38643174 PMCID: PMC11032345 DOI: 10.1038/s41598-024-59501-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 04/11/2024] [Indexed: 04/22/2024] Open
Abstract
Activity cliffs (ACs) are pairs of structurally similar molecules with significantly different affinities for a biotarget, posing a challenge in computer-assisted drug discovery. This study focuses on protein kinases, significant therapeutic targets, with some exhibiting ACs while others do not despite numerous inhibitors. The hypothesis that the presence of ACs is dependent on the target protein and its complete structural context is explored. Machine learning models were developed to link protein properties to ACs, revealing specific tripeptide sequences and overall protein properties as critical factors in ACs occurrence. The study highlights the importance of considering the entire protein matrix rather than just the binding site in understanding ACs. This research provides valuable insights for drug discovery and design, paving the way for addressing ACs-related challenges in modern computational approaches.
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Affiliation(s)
- Safa Daoud
- Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmacy, Applied Sciences Private University, Amman, Jordan.
| | - Mutasem Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman, Jordan.
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16
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Meng Q, Moinuddin SGA, Celoy RM, Smith CA, Young RP, Costa MA, Freeman RA, Fukaya M, Kim DN, Cort JR, Hawes MC, van Etten HD, Pandey P, Chittiboyina AG, Ferreira D, Davin LB, Lewis NG. Dirigent isoflavene-forming PsPTS2: 3D structure, stereochemical, and kinetic characterization comparison with pterocarpan-forming PsPTS1 homolog in pea. J Biol Chem 2024; 300:105647. [PMID: 38219818 PMCID: PMC10882141 DOI: 10.1016/j.jbc.2024.105647] [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: 08/03/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/16/2024] Open
Abstract
Pea phytoalexins (-)-maackiain and (+)-pisatin have opposite C6a/C11a configurations, but biosynthetically how this occurs is unknown. Pea dirigent-protein (DP) PsPTS2 generates 7,2'-dihydroxy-4',5'-methylenedioxyisoflav-3-ene (DMDIF), and stereoselectivity toward four possible 7,2'-dihydroxy-4',5'-methylenedioxyisoflavan-4-ol (DMDI) stereoisomers was investigated. Stereoisomer configurations were determined using NMR spectroscopy, electronic circular dichroism, and molecular orbital analyses. PsPTS2 efficiently converted cis-(3R,4R)-DMDI into DMDIF 20-fold faster than the trans-(3R,4S)-isomer. The 4R-configured substrate's near β-axial OH orientation significantly enhanced its leaving group abilities in generating A-ring mono-quinone methide (QM), whereas 4S-isomer's α-equatorial-OH was a poorer leaving group. Docking simulations indicated that the 4R-configured β-axial OH was closest to Asp51, whereas 4S-isomer's α-equatorial OH was further away. Neither cis-(3S,4S)- nor trans-(3S,4R)-DMDIs were substrates, even with the former having C3/C4 stereochemistry as in (+)-pisatin. PsPTS2 used cis-(3R,4R)-7,2'-dihydroxy-4'-methoxyisoflavan-4-ol [cis-(3R,4R)-DMI] and C3/C4 stereoisomers to give 2',7-dihydroxy-4'-methoxyisoflav-3-ene (DMIF). DP homologs may exist in licorice (Glycyrrhiza pallidiflora) and tree legume Bolusanthus speciosus, as DMIF occurs in both species. PsPTS1 utilized cis-(3R,4R)-DMDI to give (-)-maackiain 2200-fold more efficiently than with cis-(3R,4R)-DMI to give (-)-medicarpin. PsPTS1 also slowly converted trans-(3S,4R)-DMDI into (+)-maackiain, reflecting the better 4R configured OH leaving group. PsPTS2 and PsPTS1 provisionally provide the means to enable differing C6a and C11a configurations in (+)-pisatin and (-)-maackiain, via identical DP-engendered mono-QM bound intermediate generation, which PsPTS2 either re-aromatizes to give DMDIF or PsPTS1 intramolecularly cyclizes to afford (-)-maackiain. Substrate docking simulations using PsPTS2 and PsPTS1 indicate cis-(3R,4R)-DMDI binds in the anti-configuration in PsPTS2 to afford DMDIF, and the syn-configuration in PsPTS1 to give maackiain.
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Affiliation(s)
- Qingyan Meng
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Syed G A Moinuddin
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Rhodesia M Celoy
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Clyde A Smith
- Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California, USA
| | - Robert P Young
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Michael A Costa
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Rachel A Freeman
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Masashi Fukaya
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Doo Nam Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - John R Cort
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Martha C Hawes
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Hans D van Etten
- School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Pankaj Pandey
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA
| | - Amar G Chittiboyina
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA
| | - Daneel Ferreira
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA; Division of Pharmacognosy, Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, Mississippi, USA
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA.
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17
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Bandyopadhyay A, Hazra R, Roy D, Bhattacharya A. HSA over BSA: Selective detection of Human Serum Albumin via a naphtho [2,1-b] furan-based system. Chem Asian J 2024; 19:e202301055. [PMID: 38192093 DOI: 10.1002/asia.202301055] [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: 11/27/2023] [Revised: 12/29/2023] [Accepted: 01/08/2024] [Indexed: 01/10/2024]
Abstract
Human serum albumin (HSA) is an important biomarker that can be used for the early diagnosis of many diseases. In this work, a TICT probe bearing fused naphtho-furan scaffold (NPNF) was developed and employed in the selective turn-on sensing of HSA. The probe's selectivity towards HSA was observed using steady-state fluorescence experiments, with limit of quantitation in micromolar levels. NPNF's capability to exclusively detect HSA over BSA was further studied/rationalized using anisotropy and time-resolved studies. Molecular docking was used to shed light on the location of NPNF in the subdomain IB of HSA. The practical application of the probe was also demonstrated by the detection of HSA in urine and the HSA-assisted detection of cerium.
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Affiliation(s)
- Anamika Bandyopadhyay
- Department of Chemistry, Birla Institute of Technology and Science-Pilani (Hyderabad Campus), Hyderabad, 500078, India
| | - Rituparna Hazra
- Department of Chemistry, Birla Institute of Technology and Science-Pilani (Hyderabad Campus), Hyderabad, 500078, India
| | - Durba Roy
- Department of Chemistry, Birla Institute of Technology and Science-Pilani (Hyderabad Campus), Hyderabad, 500078, India
| | - Anupam Bhattacharya
- Department of Chemistry, Birla Institute of Technology and Science-Pilani (Hyderabad Campus), Hyderabad, 500078, India
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18
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Wang J, Xu Y, Wang X, Li J, Hua Z. Mechanism of Mutation-Induced Effects on the Catalytic Function of TEV Protease: A Molecular Dynamics Study. Molecules 2024; 29:1071. [PMID: 38474583 DOI: 10.3390/molecules29051071] [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: 01/27/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Tobacco etch virus protease (TEVp) is wildly exploited for various biotechnological applications. These applications take advantage of TEVp's ability to cleave specific substrate sequences to study protein function and interactions. A major limitation of this enzyme is its relatively slow catalytic rate. In this study, MD simulations were conducted on TEV enzymes and known highly active mutants (eTEV and uTEV3) to explore the relationship between mutation, conformation, and catalytic function. The results suggest that mutations distant from the active site can influence the substrate-binding pocket through interaction networks. MD analysis of eTEV demonstrates that, by stabilizing the orientation of the substrate at the catalytic site, mutations that appropriately enlarge the substrate-binding pocket will be beneficial for Kcat, enhancing the catalytic efficiency of the enzyme. On the contrary, mutations in uTEV3 reduced the flexibility of the active pocket and increased the hydrogen bonding between the substrate and enzyme, resulting in higher affinity. At the same time, the MD simulation demonstrates that mutations outside of the active site residues could affect the dynamic movement of the binding pocket by altering residue networks and communication pathways, thereby having a profound impact on reactivity. These findings not only provide a molecular mechanistic explanation for the excellent mutants, but also serve as a guiding framework for rational computational design.
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Affiliation(s)
- Jingyao Wang
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Yicong Xu
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Xujian Wang
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiahuang Li
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
- Changzhou High-Tech Research Institute, Nanjing University, Changzhou 213164, China
| | - Zichun Hua
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, China
- Changzhou High-Tech Research Institute, Nanjing University, Changzhou 213164, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing 210023, China
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19
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Du L, Zhao J, Xie N, Xie H, Xu J, Bao X, Zhou Y, Liu H, Wu X, Hu X, He T, Xu S, Zheng Y. Protective effect and mechanism of Qingfei Paidu decoction on myocardial damage mediated by influenza viruses. Front Pharmacol 2024; 15:1309682. [PMID: 38476329 PMCID: PMC10927722 DOI: 10.3389/fphar.2024.1309682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Introduction: Significant attention has been paid to myocardial damage mediated by the single-stranded RNA virus. Qingfei Paidu decoction (QFPDD) has been proved to protect the damage caused by the influenza virus A/PR/8/1934 (PR8), but its specific mechanism is unclear. Methods: Molecular biological methods, together with network pharmacology, were used to analyze the effects and underlying mechanism of QFPDD treatment on PR8-induced myocardial damage to obtain insights into the treatment of COVID-19-mediated myocardial damage. Results: Increased apoptosis and subcellular damage were observed in myocardial cells of mice infected by PR8. QFPDD treatment significantly inhibited the apoptosis and subcellular damage induced by the PR8 virus. The inflammatory factors IFN-β, TNF-α, and IL-18 were statistically increased in the myocardia of the mice infected by PR8, and the increase in inflammatory factors was prevented by QFPDD treatment. Furthermore, the expression levels or phosphorylation of necroptosis-related proteins RIPK1, RIPK3, and MLKL were abnormally elevated in the group of infected mice, while QFPDD restored the levels or phosphorylation of these proteins. Our study demonstrated that HIF-1α is a key target of QFPDD in the treatment of influenza virus-mediated injury. The HIF-α level was significantly increased by PR8 infection. Both the knockdown of HIF-1α and treatment of the myocardial cell with QFPDD significantly reversed the increased inflammatory factors during infection. Overexpression of HIF-1α reversed the inhibition effects of QFPDD on cytokine expression. Meanwhile, seven compounds from QFPDD may target HIF-1α. Conclusion: QFPDD can ameliorate influenza virus-mediated myocardial damage by reducing the degree of cell necroptosis and apoptosis, inhibiting inflammatory response and the expression of HIF-1α. Thus, our results provide new insights into the treatment of respiratory virus-mediated myocardial damage.
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Affiliation(s)
- Lijuan Du
- Department of Physiology and Pathophysiology, Health Science Center, Ningbo University, Ningbo, China
- Faculty of Physical Education, Ningbo University, Ningbo, Zhejiang, China
| | - Jing Zhao
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Nanxi Xie
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Huangze Xie
- Department of Physiology and Pathophysiology, Health Science Center, Ningbo University, Ningbo, China
| | - Jiating Xu
- Department of Physiology and Pathophysiology, Health Science Center, Ningbo University, Ningbo, China
| | - Xiaoming Bao
- Department of Cardiology, Ningbo No.2 Hospital, Ningbo, Zhejiang, China
| | - Yingsong Zhou
- Faculty of Physical Education, Ningbo University, Ningbo, Zhejiang, China
| | - Hui Liu
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiao Wu
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xin Hu
- Department of Physiology and Pathophysiology, Health Science Center, Ningbo University, Ningbo, China
| | - Tianyi He
- Department of Physiology and Pathophysiology, Health Science Center, Ningbo University, Ningbo, China
| | - Shujun Xu
- Department of Physiology and Pathophysiology, Health Science Center, Ningbo University, Ningbo, China
| | - Yuejuan Zheng
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Center for Traditional Chinese Medicine and Immunology Research, School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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20
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Wiley AM, Yang J, Madhani R, Nath A, Totah RA. Investigating the association between CYP2J2 inhibitors and QT prolongation: a literature review. Drug Metab Rev 2024; 56:145-163. [PMID: 38478383 DOI: 10.1080/03602532.2024.2329928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Drug withdrawal post-marketing due to cardiotoxicity is a major concern for drug developers, regulatory agencies, and patients. One common mechanism of cardiotoxicity is through inhibition of cardiac ion channels, leading to prolongation of the QT interval and sometimes fatal arrythmias. Recently, oxylipin signaling compounds have been shown to bind to and alter ion channel function, and disruption in their cardiac levels may contribute to QT prolongation. Cytochrome P450 2J2 (CYP2J2) is the predominant CYP isoform expressed in cardiomyocytes, where it oxidizes arachidonic acid to cardioprotective epoxyeicosatrienoic acids (EETs). In addition to roles in vasodilation and angiogenesis, EETs bind to and activate various ion channels. CYP2J2 inhibition can lower EET levels and decrease their ability to preserve cardiac rhythm. In this review, we investigated the ability of known CYP inhibitors to cause QT prolongation using Certara's Drug Interaction Database. We discovered that among the multiple CYP isozymes, CYP2J2 inhibitors were more likely to also be QT-prolonging drugs (by approximately 2-fold). We explored potential binding interactions between these inhibitors and CYP2J2 using molecular docking and identified four amino acid residues (Phe61, Ala223, Asn231, and Leu402) predicted to interact with QT-prolonging drugs. The four residues are located near the opening of egress channel 2, highlighting the potential importance of this channel in CYP2J2 binding and inhibition. These findings suggest that if a drug inhibits CYP2J2 and interacts with one of these four residues, then it may have a higher risk of QT prolongation and more preclinical studies are warranted to assess cardiovascular safety.
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Affiliation(s)
- Alexandra M Wiley
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Jade Yang
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Rivcka Madhani
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Abhinav Nath
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Rheem A Totah
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
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21
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Wang Y, Xing S, Zhao X, Chen X, Zhan CG. Unraveling the allosteric mechanisms of prolyl endopeptidases for celiac disease therapy: Insights from molecular dynamics simulations. Int J Biol Macromol 2024; 259:129313. [PMID: 38216012 DOI: 10.1016/j.ijbiomac.2024.129313] [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: 10/13/2023] [Revised: 12/26/2023] [Accepted: 01/05/2024] [Indexed: 01/14/2024]
Abstract
Prolyl endopeptidases (PEP) from Sphingomonas capsulata (sc) and Myxococcus xanthus (mx) selectively degrade gluten peptides in vitro, offering a potential therapeutic strategy for celiac disease. However, the mechanisms governing the interaction of these enzymes with their substrates remain unclear. In this study, conventional molecular dynamics simulations with a microsecond timescale and targeted molecular dynamics simulations were performed to investigate the native states of mxPEP and scPEP enzymes, as well as their allosteric binding with a representative substrate, namely, Z-Ala-Pro-p-nitroanilide (pNA). The simulations reveal that the native scPEP is in an open state, while the native mxPEP is in a closed state. When pNA approaches a closed mxPEP, it binds to an allosteric pocket located at the first and second β-sheet of the β-propeller domain, inducing the opening of this enzyme. Neither enzyme is active in the open or partly-open states. Enzymatic activity is enabled only when the catalytic pocket in the closed state fully accommodates the substrates. The internal capacity of the catalytic pocket of PEP in the closed state determines the maximum size of the gluten peptides that the enzymes can catalyze. The present work provides essential molecular dynamics information for the redesign or engineering of PEP enzymes.
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Affiliation(s)
- Yongqiang Wang
- College of Chemistry and Material Science, South Central Minzu University, Wuhan 430074, China
| | - Suting Xing
- Dongming Petrochemical, Dongming 274500, China
| | - Xinyun Zhao
- College of Chemistry and Material Science, South Central Minzu University, Wuhan 430074, China
| | - Xi Chen
- College of Chemistry and Material Science, South Central Minzu University, Wuhan 430074, China.
| | - Chang-Guo Zhan
- College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA.
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22
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Nowak D, Huczyński A, Bachorz RA, Hoffmann M. Machine Learning Application for Medicinal Chemistry: Colchicine Case, New Structures, and Anticancer Activity Prediction. Pharmaceuticals (Basel) 2024; 17:173. [PMID: 38399388 PMCID: PMC10892630 DOI: 10.3390/ph17020173] [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: 11/20/2023] [Revised: 01/02/2024] [Accepted: 01/12/2024] [Indexed: 02/25/2024] Open
Abstract
In the contemporary era, the exploration of machine learning (ML) has gained widespread attention and is being leveraged to augment traditional methodologies in quantitative structure-activity relationship (QSAR) investigations. The principal objective of this research was to assess the anticancer potential of colchicine-based compounds across five distinct cell lines. This research endeavor ultimately sought to construct ML models proficient in forecasting anticancer activity as quantified by the IC50 value, while concurrently generating innovative colchicine-derived compounds. The resistance index (RI) is computed to evaluate the drug resistance exhibited by LoVo/DX cells relative to LoVo cancer cell lines. Meanwhile, the selectivity index (SI) is computed to determine the potential of a compound to demonstrate superior efficacy against tumor cells compared to its toxicity against normal cells, such as BALB/3T3. We introduce a novel ML system adept at recommending novel chemical structures predicated on known anticancer activity. Our investigation entailed the assessment of inhibitory capabilities across five cell lines, employing predictive models utilizing various algorithms, including random forest, decision tree, support vector machines, k-nearest neighbors, and multiple linear regression. The most proficient model, as determined by quality metrics, was employed to predict the anticancer activity of novel colchicine-based compounds. This methodological approach yielded the establishment of a library encompassing new colchicine-based compounds, each assigned an IC50 value. Additionally, this study resulted in the development of a validated predictive model, capable of reasonably estimating IC50 values based on molecular structure input.
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Affiliation(s)
- Damian Nowak
- Department of Quantum Chemistry, Faculty of Chemistry, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland
| | - Adam Huczyński
- Department of Medical Chemistry, Faculty of Chemistry, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland;
| | - Rafał Adam Bachorz
- Institute of Medical Biology of Polish Academy of Sciences, Lodowa 106, 93-232 Lodz, Poland;
- Institute of Computing Science, Faculty of Computing, Poznań University of Technology, Piotrowo 2, 60-965 Poznań, Poland
| | - Marcin Hoffmann
- Department of Quantum Chemistry, Faculty of Chemistry, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland
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23
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Khalymbadzha IA, Fatykhov RF, Butorin II, Sharapov AD, Potapova AP, Muthipeedika NJ, Zyryanov GV, Melekhin VV, Tokhtueva MD, Deev SL, Kukhanova MK, Mochulskaya NN, Tsurkan MV. Bioinspired Pyrano[2,3- f]chromen-8-ones: Ring C-Opened Analogues of Calanolide A: Synthesis and Anti-HIV-1 Evaluation. Biomimetics (Basel) 2024; 9:44. [PMID: 38248618 PMCID: PMC10813249 DOI: 10.3390/biomimetics9010044] [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: 12/08/2023] [Revised: 12/23/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
We have designed and synthesized a series of bioinspired pyrano[2,3-f]coumarin-based Calanolide A analogs with anti-HIV activity. The design of these new calanolide analogs involved incorporating nitrogen heterocycles or aromatic groups in lieu of ring C, effectively mimicking and preserving their bioactive properties. Three directions for the synthesis were explored: reaction of 5-hydroxy-2,2-dimethyl-10-propyl-2H,8H-pyrano[2,3-f]chromen-8-one with (i) 1,2,4-triazines, (ii) sulfonylation followed by Suzuki cross-coupling with (het)aryl boronic acids, and (iii) aminomethylation by Mannich reaction. Antiviral assay of the synthesized compounds showed that compound 4 has moderate activity against HIV-1 on enzymes and poor activity on the cell model. A molecular docking study demonstrates a good correlation between in silico and in vitro HIV-1 reverse transcriptase (RT) activity of the compounds when docked to the nonnucleoside RT inhibitor binding site, and alternative binding modes of the considered analogs of Calanolide A were established.
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Affiliation(s)
- Igor A. Khalymbadzha
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Ramil F. Fatykhov
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Ilya I. Butorin
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Ainur D. Sharapov
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Anastasia P. Potapova
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Nibin Joy Muthipeedika
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Grigory V. Zyryanov
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Vsevolod V. Melekhin
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
- Department of Medical Biology and Genetics, Ural State Medical University, 620028 Yekaterinburg, Russia
| | - Maria D. Tokhtueva
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Sergey L. Deev
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | | | - Nataliya N. Mochulskaya
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
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24
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Flachsenberg F, Ehrt C, Gutermuth T, Rarey M. Redocking the PDB. J Chem Inf Model 2024; 64:219-237. [PMID: 38108627 DOI: 10.1021/acs.jcim.3c01573] [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: 12/19/2023]
Abstract
Molecular docking is a standard technique in structure-based drug design (SBDD). It aims to predict the 3D structure of a small molecule in the binding site of a receptor (often a protein). Despite being a common technique, it often necessitates multiple tools and involves manual steps. Here, we present the JAMDA preprocessing and docking workflow that is easy to use and allows fully automated docking. We evaluate the JAMDA docking workflow on binding sites extracted from the complete PDB and derive key factors determining JAMDA's docking performance. With that, we try to remove most of the bias due to manual intervention and provide a realistic estimate of the redocking performance of our JAMDA preprocessing and docking workflow for any PDB structure. On this large PDBScan22 data set, our JAMDA workflow finds a pose with an RMSD of at most 2 Å to the crystal ligand on the top rank for 30.1% of the structures. When applying objective structure quality filters to the PDBScan22 data set, the success rate increases to 61.8%. Given the prepared structures from the JAMDA preprocessing pipeline, both JAMDA and the widely used AutoDock Vina perform comparably on this filtered data set (the PDBScan22-HQ data set).
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Affiliation(s)
- Florian Flachsenberg
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| | - Christiane Ehrt
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| | - Torben Gutermuth
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
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25
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Cao Y, Shan Y, Wang G, Wu Z, Wang H, Wu S, Yin Z, Wei J, Bao W. Integrated of multi-omics and molecular docking reveal PHGDH, PSAT1 and PSPH in the serine synthetic pathway as potential targets of T-2 toxin exposure in pig intestinal tract. Int J Biol Macromol 2023; 253:126647. [PMID: 37678681 DOI: 10.1016/j.ijbiomac.2023.126647] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/15/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
T-2 toxin (T-2) with a molecular weight of 466.52 g/mol is an inevitable mycotoxin in food products and feeds, posing a significant threat to human and animal health. However, the underlying molecular mechanisms of the cytotoxic effects of T-2 exposure on porcine intestinal epithelial cells (IPEC-J2) remain unclear. Here, we investigated the cytotoxic effects of T-2 exposure on IPEC-J2 through the detection of cell viability, cell morphology, mitochondrial membrane potential, ROS, apoptosis and autophagy. Further transcriptomic and proteomic analyses of IPEC-J2 upon T-2 exposure were performed by using RNA-seq and TMT techniques. A total of 546 differential expressed genes (DEGs) and 269 differentially expressed proteins (DEPs) were detected. Among these, 24 common DEGs/DEPs were involved in IPEC-J2 upon T-2 exposure. Interestingly, molecular docking analysis revealed potential interactions between T-2 and three key enzymes (PHGDP, PSAT1, and PSPH) in the serine biosynthesis pathway. Besides, further experimental showed that PSAT1 knockdown exacerbated T-2-induced oxidative damage. Together, our findings indicated that the serine biosynthesis pathway including PHGDP, PSAT1, PSPH genes probably acts critical roles in the regulation of T-2-induced cell damage. This study provided new insights into the global molecular effects of T-2 exposure and identified the serine biosynthesis pathway as molecular targets and potential treatment strategies against T-2.
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Affiliation(s)
- Yue Cao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yiyi Shan
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Guangzheng Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhengchang Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Haifei Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit 48202, United States
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou University, Yangzhou 225009, China.
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26
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Bello-Vargas E, Leyva-Peralta MA, Gómez-Sandoval Z, Ordóñez M, Razo-Hernández RS. A Computational Method for the Binding Mode Prediction of COX-1 and COX-2 Inhibitors: Analyzing the Union of Coxibs, Oxicams, Propionic and Acetic Acids. Pharmaceuticals (Basel) 2023; 16:1688. [PMID: 38139814 PMCID: PMC10747940 DOI: 10.3390/ph16121688] [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: 10/06/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Among the biological targets extensively investigated to improve inflammation and chronic inflammatory conditions, cyclooxygenase enzymes (COXs) occupy a prominent position. The inhibition of these enzymes, essential for mitigating inflammatory processes, is chiefly achieved through Non-Steroidal Anti-Inflammatory Drugs (NSAIDs). In this work, we introduce a novel method-based on computational molecular docking-that could aid in the structure-based design of new compounds or the description of the anti-inflammatory activity of already-tested compounds. For this, we used eight crystal complexes (four COX-1 and COX-2 each), and each pair had a specific NSAID: Celecoxib, Meloxicam, Ibuprofen, and Indomethacin. This selection was based on the ligand selectivity towards COX-1 or COX-2 and their binding mode. An interaction profile of each NSAID was compiled to detect the residues that are key for their binding mode, highlighting the interaction made by the Me group. Furthermore, we rigorously validated our models based on structural accuracy (RMSD < 1) and (R2 > 70) using eight NSAIDs and thirteen compounds with IC50 values for each enzyme. Therefore, this model can be used for the binding mode prediction of small and structurally rigid compounds that work as COX inhibitors or the prediction of new compounds that are designed by means of a structure-based approach.
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Affiliation(s)
- Estefany Bello-Vargas
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico;
| | - Mario Alberto Leyva-Peralta
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, H. Caborca, Sonora 83621, Mexico;
| | - Zeferino Gómez-Sandoval
- Facultad de Ciencias Químicas, Universidad de Colima, km 9 Carretera Colima-Coquimatlán, Coquimatlán 28400, Mexico;
| | - Mario Ordóñez
- Centro de Investigaciones Químicas, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico;
| | - Rodrigo Said Razo-Hernández
- Laboratorio de Quimioinformática y Diseño de Fármacos, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
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27
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Calvo-Barreiro L, Talagayev V, Pach S, Abdel-Rahman SA, Wolber G, Gabr MT. Discovery of ICOS-Targeted Small Molecules Using Pharmacophore-Based Screening. ChemMedChem 2023; 18:e202300305. [PMID: 37845178 DOI: 10.1002/cmdc.202300305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
There are currently no small molecules clinically approved as immune checkpoint modulators. Besides possessing oral bioavailability, cell-penetrating capabilities and enhanced tumor penetration compared to monoclonal antibodies (mAbs), small molecules are amenable to pharmacokinetic optimization, which allows adopting flexible dosage regimens that may avoid immune-related adverse events associated with mAbs. The interaction of inducible co-stimulator (ICOS) with its ligand (ICOS-L) plays key roles in T-cell differentiation and activation of T-cell to B-cell functions. This study represents the development and validation of a virtual screening strategy to identify small molecules that bind a novel druggable binding pocket in human ICOS. We used a lipophilic canyon in the apo-structure of ICOS and the ICOS/ICOS-L interface individually as templates for molecular dynamics simulation to generate 3D pharmacophores subsequently used for virtual screening campaigns. Our strategy was successful finding a first-in-class small molecule ICOS binder (5P, KD value=108.08±26.76 μM) and validating biophysical screening platforms for ICOS-targeted small molecules. We anticipate that future structural optimization of 5P will result in the discovery of high affinity chemical ligands for ICOS.
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Affiliation(s)
- Laura Calvo-Barreiro
- Department of Radiology, Molecular Imaging Innovations Institute (MI3), Weill Cornell Medicine, New York, NY-10065, USA
| | - Valerij Talagayev
- Molecular Design Lab, Department of Chemistry, Biology and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Königin-Luisestr. 2+4, 14195, Berlin, Germany
| | - Szymon Pach
- Molecular Design Lab, Department of Chemistry, Biology and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Königin-Luisestr. 2+4, 14195, Berlin, Germany
| | - Somaya A Abdel-Rahman
- Department of Radiology, Molecular Imaging Innovations Institute (MI3), Weill Cornell Medicine, New York, NY-10065, USA
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Gerhard Wolber
- Molecular Design Lab, Department of Chemistry, Biology and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Königin-Luisestr. 2+4, 14195, Berlin, Germany
| | - Moustafa T Gabr
- Department of Radiology, Molecular Imaging Innovations Institute (MI3), Weill Cornell Medicine, New York, NY-10065, USA
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28
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Cai T, Cai B. Network pharmacology and molecular docking reveal potential mechanism of esculetin in the treatment of ulcerative colitis. Medicine (Baltimore) 2023; 102:e35852. [PMID: 37960728 PMCID: PMC10637478 DOI: 10.1097/md.0000000000035852] [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: 08/08/2023] [Accepted: 10/09/2023] [Indexed: 11/15/2023] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disease of the colonic mucosa. Esculetin is a type of natural coumarin that has many pharmacological activities such as antioxidant, anticancer, anti-inflammatory, etc. A previous study showed that esculetin improved intestinal inflammation and reduced serum proinflammatory cytokines in UC. The present study aimed to utilize network pharmacology and molecular docking to explore the potential mechanism of esculetin against UC. The potential gene targets of esculetin were predicted through SwissTargetPrediction and Super-PRED web servers. UC-related genes were obtained from DisGeNet, OMIM, and GeneCards databases. The overlap between gene targets of esculetin and UC-related genes were identified as the potential targets of esculetin against UC. The interaction between these overlapping genes was analyzed by the STRING database and the core genes were identified by Cytoscape platform. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of the core genes were then performed. And the results of these analyses were further confirmed through molecular docking. A total of 50 overlapping genes were identified as the potential action targets of esculetin against UC. Among them, 10 genes (AKT1, STAT1, CCND1, SRC, PTGS2, EGFR, NFKB1, ESR1, MMP9, SERPINE1) were finally identified as the core genes. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis results showed that the top signaling pathway associated with the core genes of esculetin against UC was the prolactin (PRL) signaling pathway. Molecular docking results showed that esculetin has a strong binding affinity to the core genes, as well as PRL and prolactin receptor. This study suggests that esculetin may have a crucial impact on UC through the PRL signaling pathway and provides insights into the potential mechanism of esculetin in the treatment of UC, which may shed light on the mechanism and treatment of UC.
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Affiliation(s)
- Ting Cai
- Department of Nephrology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi People’s Hospital, Wuxi Medical Center, Wuxi, China
| | - Bin Cai
- Department of Anorectal Surgery, Wuxi Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
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29
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Guo F, Yang H, Bai X, Li J, Han W, Li W. Probing the mechanisms of hydrazide-based HDAC inhibitors binding to HDAC3 using Gaussian accelerated molecular dynamics (GaMD) simulations. J Biomol Struct Dyn 2023:1-14. [PMID: 37937774 DOI: 10.1080/07391102.2023.2278085] [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: 09/19/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
Histone deacetylases (HDACs) have emerged as promising targets for anticancer drug development. They regulate gene expression by removing acetyl groups from lysine residues on histone tails, leading to chromatin condensation. A hydrazide-based HDAC inhibitor, N-(4-(2-Propylhydrazine-1-carbonyl)benzyl)-1H-indole-2-carboxamide (11h), has been reported to exhibit significant in vivo antitumor activity. In comparison to the lead compound N-(4-(2-Propylhydrazine-1-carbonyl)benzyl)cinnamamide (17), compound 11h demonstrates 2- to 5-fold higher HDAC inhibition and cell-based antitumor activity. However, the inhibitory mechanism of 11h remains insufficiently explored. In this study, we conducted 500 ns Gaussian Accelerated Molecular Dynamics (GaMD) simulations on Histone deacetylase 3 (HDAC3) and two complex systems (HDAC3-17 and HDAC3-11h). Our findings revealed that upon inhibitor binding, the active pocket volume of HDAC3 undergone alterations, and the movement of the L6-loop toward the active site impeded substrate entry. Moreover, we observed a destabilization of the α-helix in the aa75-89 region of HDAC3 compared to the two complex systems, indicating partial unwinding. Notably, 11h exhibited a closer proximity of its carbonyl oxygen to the active pocket's Zn2+ metal compared to 17, increasing the likelihood of coordination with the Zn2+ metal. The analysis of protein-ligand interactions highlighted a greater number of hydrogen bonds and other interactions between 11h and the receptor protein when compared to 17, underscoring the stronger binding of 11h to HDAC3. In conclusion, our study provided theoretical insights into the inhibitory mechanism of hydrazide-based HDAC inhibitors on HDAC3, thereby contributing to the development of improved drug targets for cancer therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fangfang Guo
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun, China
| | - Hengzheng Yang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Xue Bai
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Jiaying Li
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China
| | - Wannan Li
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun, China
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30
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Udoikono AD, Agwamba EC, Louis H, Benjamin I, Ahmad I, Ejiofor EU, Ahuekwe EF, Chukwuemeka K, Adeyinka AS, Patel HM, Manicum AL, Edim M. Anti-inflammatory biomolecular activity of chlorinated-phenyldiazenyl-naphthalene-2-sulfonic acid derivatives: perception from DFT, molecular docking, and molecular dynamic simulation. J Biomol Struct Dyn 2023; 41:10136-10160. [PMID: 36519503 DOI: 10.1080/07391102.2022.2153414] [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: 08/01/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022]
Abstract
In this study, two novel derivatives of naphthalene-2-sulfonic acid: 6-(((1S,5R)-3,5-dichloro-2,4,6-triazabicyclo [z3.1.0]hex-3-en-1-yl)amino)-5-((E)-phenyldiazenyl)naphthalene-2-sulfonic acid (DTPS1) and (E)-6-((4,6-dichloro-1,3,5-triazine2-yl)amino)-4-hydroxy-3-(phenyldiazenyl)naphthalene-2-sulfonic acid (DTPS2) have been synthesized and characterized using FT-IR, UV-vis, and NMR spectroscopic techniques. Applying density functional theory (DFT) at the B3LYP, APFD, PBEPBE, HCTH, TPSSTPSS, and ωB97XD/aug-cc-pVDZ level of theories for the electronic structural properties. In-vitro analysis, molecular docking, molecular dynamic (MD) simulation of the compounds was conducted to investigate the anti-inflammatory potential using COXs enzymes. Docking indicates binding affinity of -9.57, -9.60, -6.77 and -7.37 kcal/mol for DTPS1, DTPS2, Ibuprofen and Diclofenac which agrees with in-vitro assay. Results of MD simulation, indicates sulphonic group in DTPS1 has > 30% interaction with the hydroxyl and oxygen atoms in amino acid residues, but > 35% interaction with the DTPS2. It can be said that the DTPS1 and DTPS2 can induce inhibitory effect on COXs to halt biosynthesis of prostaglandins (PGs), a chief mediator of inflammation and pain in mammals.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Akaninyene D Udoikono
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Ernest C Agwamba
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Chemical Sciences, Clifford University Owerrinta, Nigeria
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Innocent Benjamin
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
| | - Iqrar Ahmad
- Department of Biological Sciences, Covenant University, Ota, Nigeria
| | - Emmanuel U Ejiofor
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Chemical Sciences, Clifford University Owerrinta, Nigeria
| | - Eze F Ahuekwe
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Biological Sciences, Covenant University, Ota, Nigeria
| | - Kelechi Chukwuemeka
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Chemical Sciences, Clifford University Owerrinta, Nigeria
| | - Adedapo S Adeyinka
- Research Centre for Synthesis and Catalysis, Department of Chemical Sciences, University of Johannesburg, Johannesburg, South Africa
| | - Harun M Patel
- Department of Biological Sciences, Covenant University, Ota, Nigeria
- Division of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Amanda-Lee Manicum
- Department of Chemistry, Tshwane University of Technology, Pretoria, South Africa
| | - Moses Edim
- Cross River State University of Technology, Calabar, Nigeria
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31
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Feng C, Fang H, Wang F, Chen W, Xia LC, Lan D, Wang Y. Crystal Structure of Fungal Nonspecific Phospholipase C Unveils a Distinct Catalytic Mechanism. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16352-16361. [PMID: 37800479 DOI: 10.1021/acs.jafc.3c05155] [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: 10/07/2023]
Abstract
Nonspecific phospholipase C (NPC) plays a pivotal role in hydrolyzing phospholipids, releasing diacylglycerol─an essential second messenger. Extensive research has elucidated the structure and function of bacterial and plant NPCs, but our understanding of their fungal counterparts remains limited. Here, we present the first crystal structure of a fungal NPC derived from Rasamsonia emersonii (RePLC), unraveling its distinguishable features divergent from other known phospholipase C. Remarkably, the structure of RePLC contains solely the phosphoesterase domain without the crucial C-terminal domain (CTD) found in plant NPCs, although CTD is important for their activity. Through a comparative analysis of structural features among NPCs from diverse species combined with structure-based mutation analyses and bioinformatics methods, we propose a potential molecular mechanism that may universally underlie the catalysis of phospholipid hydrolysis in fungal NPCs. Furthermore, our study sheds light on the captivating evolutionary trajectory of enzymes across diverse species.
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Affiliation(s)
- Chenhao Feng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Hao Fang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Fanghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Guangdong Youmei Institute of Intelligent Bio-manufacturing, Foshan 528225, China
| | - Wen Chen
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Li C Xia
- School of Mathematics, South China University of Technology, Guangzhou 510640, China
| | - Dongming Lan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Guangdong Youmei Institute of Intelligent Bio-manufacturing, Foshan 528225, China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Guangdong Youmei Institute of Intelligent Bio-manufacturing, Foshan 528225, China
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32
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Dakpa G, Kumar KJS, Nelen J, Pérez-Sánchez H, Wang SY. Antcin-B, a phytosterol-like compound from Taiwanofungus camphoratus inhibits SARS-CoV-2 3-chymotrypsin-like protease (3CL Pro) activity in silico and in vitro. Sci Rep 2023; 13:17106. [PMID: 37816832 PMCID: PMC10564890 DOI: 10.1038/s41598-023-44476-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/09/2023] [Indexed: 10/12/2023] Open
Abstract
Despite the remarkable development of highly effective vaccines, including mRNA-based vaccines, within a limited timeframe, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not been entirely eradicated. Thus, it is crucial to identify new effective anti-3CLPro compounds, pivotal for the replication of SARS-CoV-2. Here, we identified an antcin-B phytosterol-like compound from Taiwanofungus camphoratus that targets 3CLPro activity. MTT assay and ADMET prediction are employed for assessing potential cytotoxicity. Computational molecular modeling was used to screen various antcins and non-antcins for binding affinity and interaction type with 3CLPro. Further, these compounds were subjected to study their inhibitory effects on 3CLPro activity in vitro. Our results indicate that antcin-B has the best binding affinity by contacting residues like Leu141, Asn142, Glu166, and His163 via hydrogen bond and salt bridge and significantly inhibits 3CLPro activity, surpassing the positive control compound (GC376). The 100 ns molecular dynamics simulation studies showed that antcin-B formed consistent, long-lasting water bridges with Glu166 for their inhibitory activity. In summary, antcin-B could be useful to develop therapeutically viable drugs to inhibit SARS-CoV-2 replication alone or in combination with medications specific to other SARS-CoV-2 viral targets.
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Affiliation(s)
- Gyaltsen Dakpa
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 108, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - K J Senthil Kumar
- Bachelor Program of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Jochem Nelen
- Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), HiTech Innovation Hub, Universidad Católica de Murcia (UCAM), 30107, Murcia, Spain
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), HiTech Innovation Hub, Universidad Católica de Murcia (UCAM), 30107, Murcia, Spain
| | - Sheng-Yang Wang
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 108, Taiwan.
- Department of Forestry, National Chung Hsing University, Taichung, 402, Taiwan.
- Special Crop and Metabolome Discipline Cluster, Academy of Circle Economy, National Chung Hsing University, Taichung, 402, Taiwan.
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 108, Taiwan.
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33
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Shao Y, Wang Z, Wu J, Lu Y, Chen Y, Zhang H, Huang C, Shen H, Xu L, Fu Z. Unveiling immunogenic cell death-related genes in colorectal cancer: an integrated study incorporating transcriptome and Mendelian randomization analyses. Funct Integr Genomics 2023; 23:316. [PMID: 37789099 DOI: 10.1007/s10142-023-01238-2] [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: 08/10/2023] [Revised: 09/06/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023]
Abstract
Immunogenic cell death (ICD), a type of cell death that activates the tumor-specific immune response and thus exerts anti-tumor effects, is an emerging target in tumor therapy, but research on ICD-related genes (ICDGs) in colorectal cancer (CRC) remains limited. This study aimed to identify the CRC-specific ICDGs and explore their potential roles. Through RNA sequencing for tissue samples from CRC patients and integration with The Cancer Genome Atlas (TCGA) data, we identified 33 differentially expressed ICDGs in CRC. We defined the ICD score based on these genes in single-cell data, where a high score indicated an immune-active microenvironment. Additionally, molecular subtypes identified in bulk RNA data showed distinct immune landscapes. The ICD-related signature constructed with machine learning effectively distinguished patients' prognosis. The summary data-based Mendelian randomization (SMR) and colocalization analysis prioritized CFLAR for its positive association with CRC risk. Molecular docking revealed its stable binding with chemotherapeutic drugs like irinotecan. Furthermore, experimental validation confirmed CFLAR overexpression in CRC samples, and its knockdown inhibited tumor cell proliferation. Overall, this study expands the understanding of the potential roles and mechanisms of ICDGs in CRC and highlights CFLAR as a promising target for CRC.
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Affiliation(s)
- Yu Shao
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhenling Wang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jingyu Wu
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yunfei Lu
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yang Chen
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongqiang Zhang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Changzhi Huang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hengyang Shen
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lei Xu
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zan Fu
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China.
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
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Diedrich K, Krause B, Berg O, Rarey M. PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams. J Comput Aided Mol Des 2023; 37:491-503. [PMID: 37515714 PMCID: PMC10440272 DOI: 10.1007/s10822-023-00522-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/13/2023] [Indexed: 07/31/2023]
Abstract
In this article, we present PoseEdit, a new, interactive frontend of the popular pose visualization tool PoseView. PoseEdit automatically produces high-quality 2D diagrams of intermolecular interactions in 3D binding sites calculated from ligands in complex with protein, DNA, and RNA. The PoseView diagrams have been improved in several aspects, most notably in their interactivity. Thanks to the easy-to-use 2D editor of PoseEdit, the diagrams are extensively editable and extendible by the user, can be merged with other diagrams, and even be created from scratch. A large variety of graphical objects in the diagram can be moved, rotated, selected and highlighted, mirrored, removed, or even newly added. Furthermore, PoseEdit enables a synchronized 2D-3D view of macromolecule-ligand complexes simplifying the analysis of structural features and interactions. The representation of individual diagram objects regarding their visualized chemical properties, like stereochemistry, and general graphical styles, like the color of interactions, can additionally be edited. The primary objective of PoseEdit is to support scientists with an enhanced way to communicate ligand binding mode information through graphical 2D representations optimized with the scientist's input in accordance with objective criteria and individual needs. PoseEdit is freely available on the ProteinsPlus web server ( https://proteins.plus ).
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Affiliation(s)
- Konrad Diedrich
- Universität Hamburg, ZBH-Center for Bioinformatics, 20146, Hamburg, Germany
| | - Bennet Krause
- Universität Hamburg, ZBH-Center for Bioinformatics, 20146, Hamburg, Germany
- Capgemini, 10785, Berlin, Germany
| | - Ole Berg
- Universität Hamburg, ZBH-Center for Bioinformatics, 20146, Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH-Center for Bioinformatics, 20146, Hamburg, Germany.
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35
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Xiao W, Xu Y, Baak JP, Dai J, Jing L, Zhu H, Gan Y, Zheng S. Network module analysis and molecular docking-based study on the mechanism of astragali radix against non-small cell lung cancer. BMC Complement Med Ther 2023; 23:345. [PMID: 37770919 PMCID: PMC10537544 DOI: 10.1186/s12906-023-04148-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/31/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Most lung cancer patients worldwide (stage IV non-small cell lung cancer, NSCLC) have a poor survival: 25%-30% patients die < 3 months. Yet, of those surviving > 3 months, 10%-15% patients survive (very) long. Astragali radix (AR) is an effective traditional Chinese medicine widely used for non-small cell lung cancer (NSCLC). However, the pharmacological mechanisms of AR on NSCLC remain to be elucidated. METHODS Ultra Performance Liquid Chromatography system coupled with Q-Orbitrap HRMS (UPLC-Q-Orbitrap HRMS) was performed for the qualitative analysis of AR components. Then, network module analysis and molecular docking-based approach was conducted to explore underlying mechanisms of AR on NSCLC. The target genes of AR were obtained from four databases including TCMSP (Traditional Chinese Medicine Systems Pharmacology) database, ETCM (The Encyclopedia of TCM) database, HERB (A high-throughput experiment- and reference-guided database of TCM) database and BATMAN-TCM (a Bioinformatics Analysis Tool for Molecular mechanism of TCM) database. NSCLC related genes were screened by GEO (Gene Expression Omnibus) database. The STRING database was used for protein interaction network construction (PIN) of AR-NSCLC shared target genes. The critical PIN were further constructed based on the topological properties of network nodes. Afterwards the hub genes and network modules were analyzed, and enrichment analysis were employed by the R package clusterProfiler. The Autodock Vina was utilized for molecular docking, and the Gromacs was utilized for molecular dynamics simulations Furthermore, the survival analysis was performed based on TCGA (The Cancer Genome Atlas) database. RESULTS Seventy-seven AR components absorbed in blood were obtained. The critical network was constructed with 1447 nodes and 28,890 edges. Based on topological analysis, 6 hub target genes and 7 functional modules were gained. were obtained including TP53, SRC, UBC, CTNNB1, EP300, and RELA. After module analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that AR may exert therapeutic effects on NSCLC by regulating JAK-STAT signaling pathway, PI3K-AKT signaling pathway, ErbB signaling pathway, as well as NFkB signaling pathway. After the intersection calculation of the hub targets and the proteins participated in the above pathways, TP53, SRC, EP300, and RELA were obtained. These proteins had good docking affinity with astragaloside IV. Furthermore, RELA was associated with poor prognosis of NSCLC patients. CONCLUSIONS This study could provide chemical component information references for further researches. The potential pharmacological mechanisms of AR on NSCLC were elucidated, promoting the clinical application of AR in treating NSCLC. RELA was selected as a promising candidate biomarker affecting the prognosis of NSCLC patients.
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Affiliation(s)
- Wenke Xiao
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yaxin Xu
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jan P Baak
- Stavanger University Hospital, Stavanger, 4068, Norway
- Dr. Med Jan Baak AS, Tananger, 4056, Norway
| | - Jinrong Dai
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Lijia Jing
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Hongxia Zhu
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yanxiong Gan
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Shichao Zheng
- School of Intelligent Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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36
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Pletzer-Zelgert J, Ehrt C, Fender I, Griewel A, Flachsenberg F, Klebe G, Rarey M. LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments. Acta Crystallogr D Struct Biol 2023; 79:837-856. [PMID: 37561404 PMCID: PMC10478636 DOI: 10.1107/s205979832300582x] [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: 04/27/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Due to the structural complexity of proteins, their corresponding crystal arrangements generally contain a significant amount of solvent-occupied space. These areas allow a certain degree of intracrystalline protein flexibility and mobility of solutes. Therefore, knowledge of the geometry of solvent-filled channels and cavities is essential whenever the dynamics inside a crystal are of interest. Especially in soaking experiments for structure-based drug design, ligands must be able to traverse the crystal solvent channels and reach the corresponding binding pockets. Unsuccessful screenings are sometimes attributed to the geometry of the crystal packing, but the underlying causes are often difficult to understand. This work presents LifeSoaks, a novel tool for analyzing and visualizing solvent channels in protein crystals. LifeSoaks uses a Voronoi diagram-based periodic channel representation which can be efficiently computed. The size and location of channel bottlenecks, which might hinder molecular diffusion, can be directly derived from this representation. This work presents the calculated bottleneck radii for all crystal structures in the PDB and the analysis of a new, hand-curated data set of structures obtained by soaking experiments. The results indicate that the consideration of bottleneck radii and the visual inspection of channels are beneficial for planning soaking experiments.
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Affiliation(s)
| | - Christiane Ehrt
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Inken Fender
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Axel Griewel
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Florian Flachsenberg
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Universität Marburg, Marbacher Weg 6-10, 35032 Marburg, Germany
| | - Matthias Rarey
- Center for Bioinformatics, Universität Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
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37
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Beck C, Ramanujam D, Vaccarello P, Widenmeyer F, Feuerherd M, Cheng CC, Bomhard A, Abikeeva T, Schädler J, Sperhake JP, Graw M, Safi S, Hoffmann H, Staab-Weijnitz CA, Rad R, Protzer U, Frischmuth T, Engelhardt S. Trimannose-coupled antimiR-21 for macrophage-targeted inhalation treatment of acute inflammatory lung damage. Nat Commun 2023; 14:4564. [PMID: 37507393 PMCID: PMC10382532 DOI: 10.1038/s41467-023-40185-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Recent studies of severe acute inflammatory lung disease including COVID-19 identify macrophages to drive pulmonary hyperinflammation and long-term damage such as fibrosis. Here, we report on the development of a first-in-class, carbohydrate-coupled inhibitor of microRNA-21 (RCS-21), as a therapeutic means against pulmonary hyperinflammation and fibrosis. MicroRNA-21 is among the strongest upregulated microRNAs in human COVID-19 and in mice with acute inflammatory lung damage, and it is the strongest expressed microRNA in pulmonary macrophages. Chemical linkage of a microRNA-21 inhibitor to trimannose achieves rapid and specific delivery to macrophages upon inhalation in mice. RCS-21 reverses pathological activation of macrophages and prevents pulmonary dysfunction and fibrosis after acute lung damage in mice. In human lung tissue infected with SARS-CoV-2 ex vivo, RCS-21 effectively prevents the exaggerated inflammatory response. Our data imply trimannose-coupling for effective and selective delivery of inhaled oligonucleotides to pulmonary macrophages and report on a first mannose-coupled candidate therapeutic for COVID-19.
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Affiliation(s)
- Christina Beck
- Institute of Pharmacology and Toxicology, Technical University of Munich (TUM), Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Deepak Ramanujam
- Institute of Pharmacology and Toxicology, Technical University of Munich (TUM), Munich, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
- RNATICS GmbH, Planegg-Martinsried, Germany
| | - Paula Vaccarello
- Institute of Pharmacology and Toxicology, Technical University of Munich (TUM), Munich, Germany
| | - Florenc Widenmeyer
- Institute of Pharmacology and Toxicology, Technical University of Munich (TUM), Munich, Germany
| | - Martin Feuerherd
- Institute of Virology, Helmholtz Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Cho-Chin Cheng
- Institute of Virology, Helmholtz Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
| | - Anton Bomhard
- Institute of Pharmacology and Toxicology, Technical University of Munich (TUM), Munich, Germany
| | - Tatiana Abikeeva
- Institute of Pharmacology and Toxicology, Technical University of Munich (TUM), Munich, Germany
| | - Julia Schädler
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan-Peter Sperhake
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Graw
- Institute of Legal Medicine, Faculty of Medicine, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Seyer Safi
- Division of Thoracic Surgery, Klinikum rechts der Isar, Technical University of Munich (TUM), Munich, Germany
| | - Hans Hoffmann
- Division of Thoracic Surgery, Klinikum rechts der Isar, Technical University of Munich (TUM), Munich, Germany
| | - Claudia A Staab-Weijnitz
- Comprehensive Pneumology Center, Institute of Lung Health and Immunity, Helmholtz Center Munich, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, Translatum Cancer Center, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Ulrike Protzer
- Institute of Virology, Helmholtz Munich, Technical University of Munich (TUM), School of Medicine, Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Thomas Frischmuth
- Baseclick GmbH, Neuried, Germany
- RNATICS GmbH, Planegg-Martinsried, Germany
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology, Technical University of Munich (TUM), Munich, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.
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38
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Kayani H, Rasheed MA, Alonazi WB, Jamil F, Hussain A, Yan C, Ahmed R, Ibrahim M. Identification and genome-wide analysis provide insights into the genetic diversity and biotechnological potentials of novel cold-adapted Acinetobacter strain. Extremophiles 2023; 27:14. [PMID: 37354217 DOI: 10.1007/s00792-023-01301-7] [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: 02/01/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Extreme cold environments, such as polar regions or high-altitude mountains, are known for their challenging conditions including low temperatures, high salinity, and limited nutrient availability. Microbes that thrive in these environments have evolved specialized strategies to survive and function under such harsh conditions. The study aims to identify, sequence the genome, perform genome assembly, and conduct a comparative genome-wide analysis of Acinetobacter sp. strain P1, which was isolated from the Batura glacier regions of Pakistan. A basic local alignment search tool of NCBI using 16 s RNA gene sequence confirmed the strain Acinetobacter following phylogenetic analysis revealed that strain P1 clustered with Acinetobacter sp. strain AcBz01. The high-throughput Genome sequencing was done by the NovaSeq 6000 sequencing system following de novo genome assembly reported 23 contigs, a genome size of 3,732,502 bp containing approximately 3489 genes and 63 RNAs (60 tRNA, 3 rRNA). The comparative genome analysis revealed that Acinetobacter sp. strain P1 exhibited the highest homology with the Acinetobacter baumannii ATCC 17978 genome and encompassed 1668 indispensable genes, 1280 conserved genes 1821 specific genes suggesting high genomic plasticity and evolutionary diversity. The genes with functional assignments include exopolysaccharide phosphotransferase enzyme, cold-shock proteins, T6SS, membrane modifications, antibiotic resistance, and set of genes related to a wide range of metabolic characteristics such as exopolysaccharides were also present. Moreover, the structural prediction analysis of EPS proteins reveals that structural flexibility allows for conformational modifications during catalysis, which boosts or increases the catalytic effectiveness at lower temperatures. Overall, the identification of Acinetobacter, a cold-adapted bacterium, offers promising applications in bioremediation, enzyme production, food preservation, pharmaceutical development, and astrobiology. Further research and exploration of these microorganisms can unlock their full biotechnological potential and contribute to various industries and scientific endeavors.
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Affiliation(s)
- Hajra Kayani
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Muhammad Asif Rasheed
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Wadi B Alonazi
- Health Administration Department, College of Business Administration, King Saud University, Riyadh, Saudi Arabia
| | - Farrukh Jamil
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Annam Hussain
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - ChangHui Yan
- Department of Computer Science, North Dakota State University Fargo United State of America, Fargo, USA
| | - Raza Ahmed
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
- Health Administration Department, College of Business Administration, King Saud University, Riyadh, Saudi Arabia
- Department of Computer Science, North Dakota State University Fargo United State of America, Fargo, USA
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Muhammad Ibrahim
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan.
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Wang H, Sang J, Ji Z, Yu Y, Wang S, Zhu Y, Li H, Wang Y, Zhu Q, Ge R. Bisphenol A Analogues Inhibit Human and Rat 11β-Hydroxysteroid Dehydrogenase 1 Depending on Its Lipophilicity. Molecules 2023; 28:4894. [PMID: 37446556 DOI: 10.3390/molecules28134894] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/15/2023] Open
Abstract
Bisphenol A (BPA) analogues substituted on the benzene ring are widely used in a variety of industrial and consumer materials. However, their effects on the glucocorticoid-metabolizing enzyme 11β-hydroxysteroid dehydrogenase 1 (11β-HSD1) remain unclear. The inhibitory effects of 6 BPA analogues on the inhibition of human and rat 11β-HSD1 were investigated. The potencies of inhibition on human 11β-HSD1 were bisphenol H (IC50, 0.75 µM) > bisphenol G (IC50, 5.06 µM) > diallyl bisphenol A (IC50, 13.36 µM) > dimethyl bisphenol A (IC50, 30.18 µM) > bisphenol A dimethyl ether (IC50, 33.08 µM) > tetramethyl bisphenol A (>100 µM). The inhibitory strength of these chemicals on rat 11β-HSD1 was much weaker than that on the human enzyme, ranging from 74.22 to 205.7 µM. All BPA analogues are mixed/competitive inhibitors of both human and rat enzymes. Molecular docking studies predict that bisphenol H and bisphenol G both bind to the active site of human 11β-HSD1, forming a hydrogen bond with catalytic residue Ser170. The bivariate correlation of IC50 values with LogP (lipophilicity), molecular weight, heavy atoms, and molecular volume revealed a significant inverse regression and the correlation of IC50 values with ΔG (low binding energy) revealed a positive regression. In conclusion, the lipophilicity, molecular weight, heavy atoms, molecular volume, and binding affinity of a BPA analogue determine the inhibitory strength of human and rat 11β-HSD isoforms.
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Affiliation(s)
- Hong Wang
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province and Key Laboratory of Male Health and Environment of Wenzhou, Wenzhou 325000, China
| | - Jianmin Sang
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
| | - Zhongyao Ji
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
| | - Yang Yu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
| | - Shaowei Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Yang Zhu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
| | - Huitao Li
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
| | - Yiyan Wang
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
| | - Qiqi Zhu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
| | - Renshan Ge
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Wenzhou 325027, China
- Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province and Key Laboratory of Male Health and Environment of Wenzhou, Wenzhou 325000, China
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Shin SH, Hur G, Kim NR, Park JHY, Lee KW, Yang H. A machine learning-integrated stepwise method to discover novel anti-obesity phytochemicals that antagonize the glucocorticoid receptor. Food Funct 2023; 14:1869-1883. [PMID: 36723137 DOI: 10.1039/d2fo03466b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
As a type of stress hormone, glucocorticoids (GCs) affect numerous physiological pathways by binding to the glucocorticoid receptor (GR) and regulating the transcription of various genes. However, when GCs are dysregulated, the resulting hypercortisolism may contribute to various metabolic disorders, including obesity. Thus, attempts have been made to discover potent GR antagonists that can reverse excess-GC-related metabolic diseases. Phytochemicals are a collection of valuable bioactive compounds that are known for their wide variety of chemotypes. Recently, various computational methods have been developed to obtain active phytochemicals that can modulate desired target proteins. In this study, we developed a workflow comprising two consecutive quantitative structure-activity relationship-based machine learning models to discover novel GR-antagonizing phytochemicals. These two models collectively identified 65 phytochemicals that bind to and antagonize GR. Of these, nine commercially available phytochemicals were validated for GR-antagonist and anti-obesity activities. In particular, we confirmed that demethylzeylasteral, a phytochemical of the Tripterygium wilfordii Radix, exhibits potent anti-obesity activity in vitro through GR antagonism.
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Affiliation(s)
- Seo Hyun Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Gihyun Hur
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Na Ra Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Jung Han Yoon Park
- Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ki Won Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea. .,Bio-MAX Institute, Seoul National University, Seoul, 08826, Republic of Korea.,Advanced Institutes of Convergence Technology, Seoul National University, Suwon, 16229, Republic of Korea
| | - Hee Yang
- Department of Food and Nutrition, Kookmin University, Seoul 02707, Republic of Korea.
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Investigating the Anticancer Activity of G-Rh1 Using In Silico and In Vitro Studies (A549 Lung Cancer Cells). MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238311. [PMID: 36500403 PMCID: PMC9890317 DOI: 10.3390/molecules27238311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022]
Abstract
Ginsenoside Rh1 (G-Rh1), a possible bioactive substance isolated from the Korean Panax ginseng Meyer, has a wide range of pharmacological effects. In this study, we have investigated the anticancer efficacy of G-Rh1 via in silico and in vitro methodologies. This study mainly focuses on the two metastatic regulators, Rho-associated protein kinase 1 (ROCK1) and RhoA, along with other standard apoptosis regulators. The ROCK1 protein is a member of the active serine/threonine kinase family that is crucial for many biological processes, including cell division, differentiation, and death, as well as many cellular processes and muscle contraction. The abnormal activation of ROCK1 kinase causes several disorders, whereas numerous studies have also shown that RhoA is expressed highly in various cancers, including colon, lung, ovarian, gastric, and liver malignancies. Hence, inhibiting both ROCK1 and RhoA will be promising in preventing metastasis. Therefore, the molecular level interaction of G-Rh1 with the ROCK1 and RhoA active site residues from the preliminary screening clearly shows its inhibitory potential. Molecular dynamics simulation and principal component analysis give essential insights for comprehending the conformational changes that result from G-Rh1 binding to ROCK1 and RhoA. Further, MTT assay was employed to examine the potential cytotoxicity in vitro against human lung cancer cells (A549) and Raw 264.7 Murine macrophage cells. Thus, G-Rh1 showed significant cytotoxicity against human lung adenocarcinoma (A549) at 100 µg/mL. In addition, we observed an elevated level of reactive oxygen species (ROS) generation, perhaps promoting cancer cell toxicity. Additionally, G-Rh1 suppressed the mRNA expression of RhoA, ROCK1, MMP1, and MMP9 in cancer cell. Accordingly, G-Rh1 upregulated the p53, Bax, Caspase 3, caspase 9 while Bcl2 is downregulated intrinsic pathway. The findings from our study propose that the anticancer activity of G-Rh1 may be related to the induction of apoptosis by the RhoA/ROCK1 signaling pathway. As a result, this study evaluated the functional drug-like compound G-Rh1 from Panax ginseng in preventing and treating lung cancer adenocarcinoma via regulating metastasis and apoptosis.
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Enhancing the Catalytic Activity of Type II L-Asparaginase from Bacillus licheniformis through Semi-Rational Design. Int J Mol Sci 2022; 23:ijms23179663. [PMID: 36077061 PMCID: PMC9456134 DOI: 10.3390/ijms23179663] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 01/10/2023] Open
Abstract
Low catalytic activity is a key factor limiting the widespread application of type II L-asparaginase (ASNase) in the food and pharmaceutical industries. In this study, smart libraries were constructed by semi-rational design to improve the catalytic activity of type II ASNase from Bacillus licheniformis. Mutants with greatly enhanced catalytic efficiency were screened by saturation mutations and combinatorial mutations. A quintuple mutant ILRAC was ultimately obtained with specific activity of 841.62 IU/mg and kcat/Km of 537.15 min−1·mM−1, which were 4.24-fold and 6.32-fold more than those of wild-type ASNase. The highest specific activity and kcat/Km were firstly reported in type II ASNase from Bacillus licheniformis. Additionally, enhanced pH stability and superior thermostability were both achieved in mutant ILRAC. Meanwhile, structural alignment and molecular dynamic simulation demonstrated that high structure stability and strong substrate binding were beneficial for the improved thermal stability and enzymatic activity of mutant ILRAC. This is the first time that enzymatic activity of type II ASNase from Bacillus licheniformis has been enhanced by the semi-rational approach, and results provide new insights into enzymatic modification of L-asparaginase for industrial applications.
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