1
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Santini BL, Gaardløs M, Wyrzykowski D, Rothemund S, Penk A, Zacharias M, Samsonov SA. Rational design of glycosaminoglycan binding cyclic peptides using cPEPmatch. Comput Struct Biotechnol J 2024; 23:2985-2994. [PMID: 39135886 PMCID: PMC11318538 DOI: 10.1016/j.csbj.2024.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 07/19/2024] [Accepted: 07/19/2024] [Indexed: 08/15/2024] Open
Abstract
Cyclic peptides present a robust platform for drug design, offering high specificity and stability due to their conformationally constrained structures. In this study, we introduce an updated version of the Cyclic Peptide Matching program (cPEPmatch) tailored for the identification of cyclic peptides capable of mimicking protein-glycosaminoglycan (GAG) binding sites. We focused on engineering cyclic peptides to replicate the GAG-binding affinity of antithrombin III (ATIII), a protein that plays a crucial role in modulating anticoagulation through interaction with the GAG heparin. By integrating computational and experimental methods, we successfully identified a cyclic peptide binder with promising potential for future optimization. MD simulations and MM-GBSA calculations were used to assess binding efficacy, supplemented by umbrella sampling to approximate free energy landscapes. The binding specificity was further validated through NMR and ITC experiments. Our findings demonstrate that the computationally designed cyclic peptides effectively target GAGs, suggesting their potential as novel therapeutic agents. This study advances our understanding of peptide-GAG interactions and lays the groundwork for future development of cyclic peptide-based therapeutics.
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Affiliation(s)
- Brianda L. Santini
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, Garching, Germany
| | | | | | - Sven Rothemund
- Unit Peptide Technologies, Liebigstraße 21, Leipzig, Germany
| | - Anja Penk
- Institute of Medical Physics and Biophysics, Härtelstr. 16/18, Leipzig, Germany
| | - Martin Zacharias
- Center for Functional Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, Garching, Germany
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2
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Xue Y, Zhong J, Liu X, Xiang D, Qin X. Improved physicochemical properties of bigels produced with ethyl cellulose-based oleogel and moderately deacetylated konjac glucomannan hydrogel. Food Chem 2024; 459:140429. [PMID: 39024880 DOI: 10.1016/j.foodchem.2024.140429] [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: 07/03/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024]
Abstract
The ideal physicochemical properties of bigels are important for food applications. Therefore, a new bigel was prepared based on mixed beef tallow and soybean oil oleogel and deacetylated konjac glucomannan (KGM) hydrogel. The effect of the deacetylation degree of KGM on the physicochemical properties and microstructure of bigels was studied. The bigel containing moderate deacetylation degree of KGM had better rheological properties and hardness (319.84 g) than that with low and high deacetylation degrees of KGM. The interactions among the bigel components were analyzed by Fourier transform infrared spectroscopy and molecular dynamics simulation, indicating that the formation of the bigels was dominated by electrostatic interactions. Overall, the bigels containing moderate deacetylation degree of KGM had better physical properties, which may provide a theoretical foundation to develop bigels with low cholesterol, trans and saturated fats levels to replace traditional solid fats in food industry.
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Affiliation(s)
- Yi Xue
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Jinfeng Zhong
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Xiong Liu
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Dao Xiang
- Chongqing Muge Food Co., Ltd., Chongqing, 401519, China
| | - Xiaoli Qin
- College of Food Science, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, China.
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3
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Pietri GP, Bertuzzi S, Karnicar K, Unione L, Lisnic B, Malic S, Miklic K, Novak M, Calloni I, Santini L, Usenik A, Romano MR, Adamo R, Jonjic S, Turk D, Jiménez-Barbero J, Lenac Rovis T. Antigenic determinants driving serogroup-specific antibody response to Neisseria meningitidis C, W, and Y capsular polysaccharides: Insights for rational vaccine design. Carbohydr Polym 2024; 341:122349. [PMID: 38876728 DOI: 10.1016/j.carbpol.2024.122349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/15/2024] [Accepted: 05/29/2024] [Indexed: 06/16/2024]
Abstract
Meningococcal glycoconjugate vaccines sourced from capsular polysaccharides (CPSs) of pathogenic Neisseria meningitidis strains are well-established measures to prevent meningococcal disease. However, the exact structural factors responsible for antibody recognition are not known. CPSs of Neisseria meningitidis serogroups Y and W differ by a single stereochemical center, yet they evoke specific immune responses. Herein, we developed specific monoclonal antibodies (mAbs) targeting serogroups C, Y, and W and evaluated their ability to kill bacteria. We then used these mAbs to dissect structural elements responsible for carbohydrate-protein interactions. First, Men oligosaccharides were screened against the mAbs using ELISA to select putative lengths representing the minimal antigenic determinant. Next, molecular interaction features between the mAbs and serogroup-specific sugar fragments were elucidated using STD-NMR. Moreover, X-ray diffraction data with the anti-MenW CPS mAb enabled the elucidation of the sugar-antibody binding mode. Our findings revealed common traits in the epitopes of all three sialylated serogroups. The minimal binding epitopes typically comprise five to six repeating units. Moreover, the O-acetylation of the neuraminic acid moieties was fundamental for mAb binding. These insights hold promise for the rational design of optimized meningococcal oligosaccharides, opening new avenues for novel production methods, including chemical or enzymatic approaches.
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Affiliation(s)
- Gian Pietro Pietri
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Sara Bertuzzi
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Katarina Karnicar
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Luca Unione
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009 Bilbao, Bizkaia, Spain
| | - Berislav Lisnic
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Suzana Malic
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Karmela Miklic
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Matej Novak
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Ilaria Calloni
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain
| | | | - Aleksandra Usenik
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | | | | | - Stipan Jonjic
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Dusan Turk
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia, Spain; Ikerbasque, Basque Foundation for Science, Euskadi Plaza 5, 48009 Bilbao, Bizkaia, Spain; Department of Organic and Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940 Leioa, Bizkaia, Spain; Centro de Investigación Biomédica En Red de Enfermedades Respiratorias, 28029 Madrid, Spain.
| | - Tihana Lenac Rovis
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.
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4
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Obukhova P, Tyrtysh T, Tsygankova S, Paramonov A, Gordeeva E, Shilova N, Lipatnikov A, Sokolova M, Henry S, Salimov E, Bovin N, Ryzhov I. Chemical Resolution of an Epitope Recognized by Blood Group Antibodies Capable of Binding Both A and B Red Blood Cells. Chembiochem 2024; 25:e202400430. [PMID: 38900551 DOI: 10.1002/cbic.202400430] [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: 05/14/2024] [Revised: 06/09/2024] [Accepted: 06/20/2024] [Indexed: 06/21/2024]
Abstract
The high specificity of human antibodies to blood group A and B antigens is impressive, especially when considering the structural difference between these antigens (tetrasaccharides) is a NHAc versus a hydroxyl group on the terminal monosaccharide residue. It is well established that in addition to anti-A and anti-B there is a third antibody, anti-A,B capable of recognizing both A and B antigens. To analyze this AB specificity, we synthesized a tetrasaccharide, where the NHAc of the A antigen was replaced with an NH2. This NH2 group was then used to attach the glycan to an affinity resin, creating an AB epitope (ABep) adsorbent where the critical site for recognition by A and B antibodies was not accessible, while the rest of the (conformationally compact) tetrasaccharide remained accessible. Anti-ABep antibodies were then isolated from blood group O donors and found to have expected A,B specificity against immobilized and red cell bound synthetic antigens, including ABep, and were able to agglutinate both A and B red cells. The amount of these anti-ABep (anti-A,B) antibodies found in the blood of group O donors was comparable to levels of anti-A and anti-B found in group B and A individuals. Using STD-NMR the location for the AB epitope on the tetrasaccharide was found.
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Affiliation(s)
- Polina Obukhova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- FSBI - National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov Ministry of Health care of the Russian Federation, Moscow, Russian Federation
| | - Tatiana Tyrtysh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Svetlana Tsygankova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander Paramonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Elena Gordeeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Nadezhda Shilova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- FSBI - National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov Ministry of Health care of the Russian Federation, Moscow, Russian Federation
| | - Alexander Lipatnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Maria Sokolova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Emin Salimov
- I. M. Sechenov First Moscow State Medical University of the Ministry of Health care of the Russian Federation (Sechenov University), Moscow, Russian Federation
| | - Nicolai Bovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ivan Ryzhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
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5
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Bojarski KK, David A, Lecaille F, Samsonov SA. In silico approaches for better understanding cysteine cathepsin-glycosaminoglycan interactions. Carbohydr Res 2024; 543:109201. [PMID: 39013335 DOI: 10.1016/j.carres.2024.109201] [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: 04/12/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/18/2024]
Abstract
Cysteine cathepsins constitute the largest cathepsin family, with 11 proteases in human that are present primarily within acidic endosomal and lysosomal compartments. They are involved in the turnover of intracellular and extracellular proteins. They are synthesized as inactive procathepsins that are converted to mature active forms. Cathepsins play important roles in physiological and pathological processes and, therefore, receive increasing attention as potential therapeutic targets. Their maturation and activity can be regulated by glycosaminoglycans (GAGs), long linear negatively charged polysaccharides composed of recurring dimeric units. In this review, we summarize recent computational progress in the field of (pro)cathepsin-GAG complexes analyses.
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Affiliation(s)
- Krzysztof K Bojarski
- Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, Gdansk, 80-233, Poland.
| | - Alexis David
- Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team "Mécanismes Protéolytiques dans l'Inflammation, Tours, France
| | - Fabien Lecaille
- Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team "Mécanismes Protéolytiques dans l'Inflammation, Tours, France
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, 80-308, Poland
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6
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Nieto-Fabregat F, Lenza MP, Marseglia A, Di Carluccio C, Molinaro A, Silipo A, Marchetti R. Computational toolbox for the analysis of protein-glycan interactions. Beilstein J Org Chem 2024; 20:2084-2107. [PMID: 39189002 PMCID: PMC11346309 DOI: 10.3762/bjoc.20.180] [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: 12/20/2023] [Accepted: 08/01/2024] [Indexed: 08/28/2024] Open
Abstract
Protein-glycan interactions play pivotal roles in numerous biological processes, ranging from cellular recognition to immune response modulation. Understanding the intricate details of these interactions is crucial for deciphering the molecular mechanisms underlying various physiological and pathological conditions. Computational techniques have emerged as powerful tools that can help in drawing, building and visualising complex biomolecules and provide insights into their dynamic behaviour at atomic and molecular levels. This review provides an overview of the main computational tools useful for studying biomolecular systems, particularly glycans, both in free state and in complex with proteins, also with reference to the principles, methodologies, and applications of all-atom molecular dynamics simulations. Herein, we focused on the programs that are generally employed for preparing protein and glycan input files to execute molecular dynamics simulations and analyse the corresponding results. The presented computational toolbox represents a valuable resource for researchers studying protein-glycan interactions and incorporates advanced computational methods for building, visualising and predicting protein/glycan structures, modelling protein-ligand complexes, and analyse MD outcomes. Moreover, selected case studies have been reported to highlight the importance of computational tools in studying protein-glycan systems, revealing the capability of these tools to provide valuable insights into the binding kinetics, energetics, and structural determinants that govern specific molecular interactions.
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Affiliation(s)
- Ferran Nieto-Fabregat
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Maria Pia Lenza
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Angela Marseglia
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Cristina Di Carluccio
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Roberta Marchetti
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
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7
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Murphy PV, Dhara A, Fitzgerald LS, Hever E, Konda S, Mandal K. Small lectin ligands as a basis for applications in glycoscience and glycomedicine. Chem Soc Rev 2024. [PMID: 39162695 DOI: 10.1039/d4cs00642a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Glycan recognition by lectins mediates important biological events. This Tutorial Review aims to introduce lectin-ligand interactions and show how these molecular recognition events inspire innovations such as: (i) glycomimetic ligands; (ii) multivalent ligand agonists/antagonists; (iii) ligands for precision delivery of therapies to cells, where therapies include vaccines, siRNA and LYTACs (iv) development of diagnostics. A small number of case studies are selected to demonstrate principles for development of new ligands for applications inspired by knowledge of natural glycan ligand structure and function.
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Affiliation(s)
- Paul V Murphy
- School of Biological and Chemical Sciences, Galway, H91TK33, Ireland.
- SSPC, SFI Research Centre for Pharmaceuticals, Galway, H91TK33, Ireland
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, University Road, Galway, H91TK33, Ireland
| | - Ashis Dhara
- School of Biological and Chemical Sciences, Galway, H91TK33, Ireland.
- SSPC, SFI Research Centre for Pharmaceuticals, Galway, H91TK33, Ireland
| | - Liam S Fitzgerald
- School of Biological and Chemical Sciences, Galway, H91TK33, Ireland.
- SSPC, SFI Research Centre for Pharmaceuticals, Galway, H91TK33, Ireland
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, University Road, Galway, H91TK33, Ireland
| | - Eoin Hever
- School of Biological and Chemical Sciences, Galway, H91TK33, Ireland.
| | - Saidulu Konda
- School of Biological and Chemical Sciences, Galway, H91TK33, Ireland.
| | - Kishan Mandal
- School of Biological and Chemical Sciences, Galway, H91TK33, Ireland.
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8
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Zhang H, Ma Y, Yuan S. Molecular Dynamics Study on Adsorption and Desorption of the Model Oligosaccharide above Polymer Antifouling Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:17320-17330. [PMID: 39119623 DOI: 10.1021/acs.langmuir.4c01353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Polysaccharide foulants play a key role in the adhesion of many fouling organisms, which may cause severe marine biofouling. However, the detailed interaction mechanism between polysaccharides and antifouling membranes is still indistinct compared with that between the fouling protein and antifouling surfaces. In this paper, a model oligosaccharide built based on the monosaccharide composition found in diatom extracellular polymeric substances (EPS) was used as a model foulant to investigate its adsorption and desorption above three T4 antifouling membranes. It was found that the anionic poly(3-(methacryloyloxy)propane-1-sulfonate) (T4-SP) antifouling membrane had excellent antifouling ability with respect to the model oligosaccharide, while the oligosaccharide can be easily adsorbed on the poly(2-(dimethylamino)ethyl methacrylate) (T4-DM) membrane with vdW attraction and on the zwitterionic poly(sulfobetaine methacrylate) (T4-SB) membrane with electrostatic attraction. As little is known about the details of polysaccharides' adsorption above antifouling membranes at the molecular level, we hope this work will serve as a theoretical basis for finding more effective materials to prevent or control marine biofouling.
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Affiliation(s)
- Heng Zhang
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Jinan 250199, P. R. China
- Shandong Chambroad Holding Co., Ltd., Binzhou 256500, Shandong, P. R. China
| | - Ying Ma
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Jinan 250199, P. R. China
| | - Shiling Yuan
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Jinan 250199, P. R. China
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9
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Phulera S, Dickson CJ, Schwalen CJ, Khoshouei M, Cassell SJ, Sun Y, Condos T, Whicher J, Weihofen WA. Scorpion α-toxin LqhαIT specifically interacts with a glycan at the pore domain of voltage-gated sodium channels. Structure 2024:S0969-2126(24)00284-3. [PMID: 39181123 DOI: 10.1016/j.str.2024.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/13/2024] [Accepted: 07/30/2024] [Indexed: 08/27/2024]
Abstract
Voltage-gated sodium (Nav) channels sense membrane potential and drive cellular electrical activity. The deathstalker scorpion α-toxin LqhαIT exerts a strong action potential prolonging effect on Nav channels. To elucidate the mechanism of action of LqhαIT, we determined a 3.9 Å cryoelectron microscopy (cryo-EM) structure of LqhαIT in complex with the Nav channel from Periplaneta americana (NavPas). We found that LqhαIT binds to voltage sensor domain 4 and traps it in an "S4 down" conformation. The functionally essential C-terminal epitope of LqhαIT forms an extensive interface with the glycan scaffold linked to Asn330 of NavPas that augments a small protein-protein interface between NavPas and LqhαIT. A combination of molecular dynamics simulations, structural comparisons, and prior mutagenesis experiments demonstrates the functional importance of this toxin-glycan interaction. These findings establish a structural basis for the specificity achieved by scorpion α-toxins and reveal the conserved glycan as an essential component of the toxin-binding epitope.
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Affiliation(s)
- Swastik Phulera
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Callum J Dickson
- Global Discovery Chemistry, Novartis Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Christopher J Schwalen
- Global Discovery Chemistry, Novartis Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Maryam Khoshouei
- Discovery Sciences, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Samantha J Cassell
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Yishan Sun
- Neuroscience, Novartis Biomedical Research, 22 Windsor St, Cambridge, MA 02139, USA
| | - Tara Condos
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jonathan Whicher
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Wilhelm A Weihofen
- Discovery Sciences, Novartis Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA.
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10
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Painter C, Sankaranarayanan NV, Nagarajan B, Mandel Clausen T, West AM, Setiawan NJ, Park J, Porell RN, Bartels PL, Sandoval DR, Vasquez GJ, Chute JP, Godula K, Vander Kooi CW, Gordts PL, Corbett KD, Termini CM, Desai UR, Esko JD. Alteration of Neuropilin-1 and Heparan Sulfate Interaction Impairs Murine B16 Tumor Growth. ACS Chem Biol 2024; 19:1820-1835. [PMID: 39099090 PMCID: PMC11334110 DOI: 10.1021/acschembio.4c00389] [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: 06/06/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/06/2024]
Abstract
Neuropilin-1 acts as a coreceptor with vascular endothelial growth factor receptors to facilitate binding of its ligand, vascular endothelial growth factor. Neuropilin-1 also binds to heparan sulfate, but the functional significance of this interaction has not been established. A combinatorial library screening using heparin oligosaccharides followed by molecular dynamics simulations of a heparin tetradecasaccharide suggested a highly conserved binding site composed of amino acid residues extending across the b1 and b2 domains of murine neuropilin-1. Mutagenesis studies established the importance of arginine513 and lysine514 for binding of heparin to a recombinant form of Nrp1 composed of the a1, a2, b1, and b2 domains. Recombinant Nrp1 protein bearing R513A,K514A mutations showed a significant loss of heparin-binding, heparin-induced dimerization, and heparin-dependent thermal stabilization. Isothermal calorimetry experiments suggested a 1:2 complex of heparin tetradecasaccharide:Nrp1. To study the impact of altered heparin binding in vivo, a mutant allele of Nrp1 bearing the R513A,K514A mutations was created in mice (Nrp1D) and crossbred to Nrp1+/- mice to examine the impact of altered heparan sulfate binding. Analysis of tumor formation showed variable effects on tumor growth in Nrp1D/D mice, resulting in a frank reduction in tumor growth in Nrp1D/- mice. Expression of mutant Nrp1D protein was normal in tissues, suggesting that the reduction in tumor growth was due to the altered binding of heparin/heparan sulfate to neuropilin-1. These findings suggest that the interaction of neuropilin-1 with heparan sulfate modulates its stability and its role in tumor formation and growth.
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Affiliation(s)
- Chelsea
D. Painter
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
| | - Nehru Viji Sankaranarayanan
- Department
of Medicinal Chemistry, Virginia Commonwealth
University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Balaji Nagarajan
- Department
of Medicinal Chemistry, Virginia Commonwealth
University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Thomas Mandel Clausen
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
| | - Alan M.V. West
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
| | - Nicollette J. Setiawan
- Translational
Science and Therapeutics Division, Fred
Hutchinson Cancer Center, Seattle, Washington 98109, United States
| | - Jeeyoung Park
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
| | - Ryan N. Porell
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Phillip L. Bartels
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Daniel R. Sandoval
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
| | - Gabriel J. Vasquez
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
| | - John P. Chute
- Samuel
Oschin Cancer Center, Cedars Sinai Medical
Center, Los Angeles, California 90048, United States
- Division
of Hematology & Cellular Therapy, Cedars
Sinai Medical Center, Los Angeles, California 90048, United States
- Regenerative
Medicine Institute, Cedars Sinai Medical
Center, Los Angeles, California 90048, United States
| | - Kamil Godula
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Craig W. Vander Kooi
- Department
of Biochemistry and Molecular Biology, University
of Florida, Gainesville, Florida 32610, United
States
| | - Philip L.S.M. Gordts
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Medicine, University of California, San
Diego, La Jolla, California 92093, United States
| | - Kevin D. Corbett
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Molecular Biology, University of California,
San Diego, La Jolla, California 92093, United States
| | - Christina M. Termini
- Translational
Science and Therapeutics Division, Fred
Hutchinson Cancer Center, Seattle, Washington 98109, United States
| | - Umesh R. Desai
- Department
of Medicinal Chemistry, Virginia Commonwealth
University, Richmond, Virginia 23298, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Jeffrey D. Esko
- Department
of Cellular and Molecular Medicine, University
of California, San Diego, La Jolla, California 92093, United States
- Glycobiology
Research and Training Center, University
of California, San Diego, La Jolla, California 92093, United States
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11
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Brossier C, Jardou M, Janaszkiewicz A, Firoud D, Petit I, Arnion H, Pinault E, Sauvage FL, Druilhe A, Picard N, Di Meo F, Marquet P, Lawson R. Gut microbiota biotransformation of drug glucuronides leading to gastrointestinal toxicity: Therapeutic potential of bacterial β-glucuronidase inhibition in mycophenolate-induced enteropathy. Life Sci 2024; 351:122792. [PMID: 38857657 DOI: 10.1016/j.lfs.2024.122792] [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: 02/09/2024] [Revised: 04/28/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
AIMS Drug-induced enteropathy is often associated with the therapeutic use of certain glucuronidated drugs. One such drug is mycophenolic acid (MPA), a well-established immunosuppressant of which gastrointestinal adverse effects are a major concern. The role of bacterial β-glucuronidase (β-G) from the gut microbiota in MPA-induced enteropathy has recently been discovered. Bacterial β-G hydrolyzes MPAG, the glucuronide metabolite of MPA excreted in the bile, leading to the digestive accumulation of MPA that would favor in turn these adverse events. We therefore hypothesized that taming bacterial β-G activity might reduce MPA digestive exposure and prevent its toxicity. MAIN METHODS By using a multiscale approach, we evaluated the effect of increasing concentrations of MPA on intestinal epithelial cells (Caco-2 cell line) viability, proliferation, and migration. Then, we investigated the inhibitory properties of amoxapine, a previously described bacterial β-G inhibitor, by using molecular dynamics simulations, and evaluated its efficiency in blocking MPAG hydrolysis in an Escherichia coli-based β-G activity assay. The pharmacological effect of amoxapine was evaluated in a mouse model. KEY FINDINGS We observed that MPA impairs intestinal epithelial cell homeostasis. Amoxapine efficiently blocks the hydrolysis of MPAG to MPA and significantly reduces digestive exposure to MPA in mice. As a result, administration of amoxapine in MPA-treated mice significantly attenuated gastrointestinal lesions. SIGNIFICANCE Collectively, these results suggest that the digestive accumulation of MPA is involved in the pathophysiology of MPA-gastrointestinal adverse effects. This study provides a proof-of-concept of the therapeutic potential of bacterial β-G inhibitors in glucuronidated drug-induced enteropathy.
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Affiliation(s)
- Clarisse Brossier
- Pharmacology & Transplantation (P&T), INSERM U1248, Université de Limoges, F-87000 Limoges, France
| | - Manon Jardou
- Pharmacology & Transplantation (P&T), INSERM U1248, Université de Limoges, F-87000 Limoges, France
| | - Angelika Janaszkiewicz
- Pharmacology & Transplantation (P&T), INSERM U1248, Université de Limoges, F-87000 Limoges, France
| | - Djouher Firoud
- Pharmacology & Transplantation (P&T), INSERM U1248, Université de Limoges, F-87000 Limoges, France
| | - Isy Petit
- Pharmacology & Transplantation (P&T), INSERM U1248, Université de Limoges, F-87000 Limoges, France
| | - Hélène Arnion
- Pharmacology & Transplantation (P&T), INSERM U1248, Université de Limoges, F-87000 Limoges, France
| | - Emilie Pinault
- Pharmacology & Transplantation (P&T), INSERM U1248, Université de Limoges, F-87000 Limoges, France
| | - François-Ludovic Sauvage
- Pharmacology & Transplantation (P&T), INSERM U1248, Université de Limoges, F-87000 Limoges, France
| | - Anne Druilhe
- Pharmacology & Transplantation (P&T), INSERM U1248, Université de Limoges, F-87000 Limoges, France
| | - Nicolas Picard
- Pharmacology & Transplantation (P&T), INSERM U1248, Université de Limoges, F-87000 Limoges, France; Department of Pharmacology, Toxicology and Pharmacovigilance, CHU Limoges, F-87000 Limoges, France
| | - Florent Di Meo
- Pharmacology & Transplantation (P&T), INSERM U1248, Université de Limoges, F-87000 Limoges, France
| | - Pierre Marquet
- Pharmacology & Transplantation (P&T), INSERM U1248, Université de Limoges, F-87000 Limoges, France; Department of Pharmacology, Toxicology and Pharmacovigilance, CHU Limoges, F-87000 Limoges, France
| | - Roland Lawson
- Pharmacology & Transplantation (P&T), INSERM U1248, Université de Limoges, F-87000 Limoges, France.
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12
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Dhurua S, Jana M. Conformational preferences of heparan sulfate to recognize the CXCL8 dimer in aqueous medium: degree of sulfation and hydrogen bonds. Phys Chem Chem Phys 2024; 26:21888-21904. [PMID: 39105690 DOI: 10.1039/d4cp01430h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
The sulfation pattern and epimerization of the long-chain sulfated polysaccharide heparan sulfate (HS) cause structural diversity and regulate various physiological and pathological processes when binding with proteins. In this work, we performed a series of molecular dynamics simulations of three variants of the octadecasaccharide HS with varying sulfation positions in aqueous medium in their free forms and in the presence of the chemokine CXCL8 dimer. The free energy of binding depicts the sulfation at the 6-O position of GlcNAc (HS6S), and both 3-O and 6-O positions of GlcNAc (HS3S6S) of HS variants are more likely to bind with the CXCL8 dimer than the triply sulfated HS2S3S6S, which is sulfated at the 2-O position of GlcUA additionally along with 3-O and 6-O positions of GlcNAc. Binding between HS and CXCL8 was driven by electrostatic and van der Waals interactions predominantly regardless of the sulfation pattern; however, unfavorable entropic contribution suppressed the interaction between HS and CXCL8. The contribution of different amino acid residues to the binding energetics suggested that basic amino acids line up the binding site of CXCL8. This study further acknowledges the role of interfacial water that is structured and bound with HS through hydrogen bonds, exhibiting differential hydrogen bond relaxation dynamics compared to when the HS molecules are free. Moreover, this study identifies that with the increase in sulfation, the HS-water hydrogen bond relaxation occurs faster with the complexation, while the reverse trend is followed in their free forms. Significant structural adaptation of the different sulfated HS molecules, as verified from the free energy landscapes generated from various reaction coordinates, root-mean-square-deviations, end-to-end distances, including ring pucker angles, dihedral flexibility, and the high conformational entropy cost arising from the glycosidic bonds, suggests that the different sulfated variants of HS undergo significant structural transformation to bind with CXCL8. The presence of a CXCL8 dimer imposes the bound forms of HS to adopt non-linear structures with skew-boat conformations. The atomistic details of the study would help in understanding the selectivity and conformational diversity, as well as the role of solvents in the recognition of CXCL8 by different sulfated variants of HS molecules.
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Affiliation(s)
- Shakuntala Dhurua
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela-769008, India.
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela-769008, India.
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13
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Takaba K, Friedman AJ, Cavender CE, Behara PK, Pulido I, Henry MM, MacDermott-Opeskin H, Iacovella CR, Nagle AM, Payne AM, Shirts MR, Mobley DL, Chodera JD, Wang Y. Machine-learned molecular mechanics force fields from large-scale quantum chemical data. Chem Sci 2024; 15:12861-12878. [PMID: 39148808 PMCID: PMC11322960 DOI: 10.1039/d4sc00690a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/17/2024] [Indexed: 08/17/2024] Open
Abstract
The development of reliable and extensible molecular mechanics (MM) force fields-fast, empirical models characterizing the potential energy surface of molecular systems-is indispensable for biomolecular simulation and computer-aided drug design. Here, we introduce a generalized and extensible machine-learned MM force field, espaloma-0.3, and an end-to-end differentiable framework using graph neural networks to overcome the limitations of traditional rule-based methods. Trained in a single GPU-day to fit a large and diverse quantum chemical dataset of over 1.1 M energy and force calculations, espaloma-0.3 reproduces quantum chemical energetic properties of chemical domains highly relevant to drug discovery, including small molecules, peptides, and nucleic acids. Moreover, this force field maintains the quantum chemical energy-minimized geometries of small molecules and preserves the condensed phase properties of peptides and folded proteins, self-consistently parametrizing proteins and ligands to produce stable simulations leading to highly accurate predictions of binding free energies. This methodology demonstrates significant promise as a path forward for systematically building more accurate force fields that are easily extensible to new chemical domains of interest.
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Affiliation(s)
- Kenichiro Takaba
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
- Pharmaceuticals Research Center, Advanced Drug Discovery, Asahi Kasei Pharma Corporation Shizuoka 410-2321 Japan
| | - Anika J Friedman
- Department of Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80309 USA
| | - Chapin E Cavender
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Pavan Kumar Behara
- Center for Neurotherapeutics, Department of Pathology and Laboratory Medicine, University of California Irvine CA 92697 USA
| | - Iván Pulido
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | - Michael M Henry
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | | | - Christopher R Iacovella
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | - Arnav M Nagle
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
- Department of Bioengineering, University of California, Berkeley Berkeley CA 94720 USA
| | - Alexander Matthew Payne
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center New York 10065 USA
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder Boulder CO 80309 USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California Irvine California 92697 USA
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
| | - Yuanqing Wang
- Simons Center for Computational Physical Chemistry and Center for Data Science, New York University New York NY 10004 USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center New York NY 10065 USA
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14
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AlRawashdeh S, Mosa FES, Barakat KH. Computational insights into the mechanisms underlying structural destabilization and recovery in trafficking-deficient hERG mutants. Front Mol Biosci 2024; 11:1341727. [PMID: 39193219 PMCID: PMC11347279 DOI: 10.3389/fmolb.2024.1341727] [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: 11/20/2023] [Accepted: 07/31/2024] [Indexed: 08/29/2024] Open
Abstract
Cardiovascular diseases are a major global health concern, responsible for a significant number of deaths each year, often linked to cardiac arrhythmias resulting from dysfunction in ion channels. Hereditary Long QT Syndrome (LQTS) is a condition characterized by a prolonged QT interval on ECG, increasing the risk of sudden cardiac death. The most common type of LQTS, LQT2, is caused by mutations in the hERG gene, affecting a potassium ion channel. The majority of these mutations disrupt the channel's trafficking to the cell membrane, leading to intracellular retention. Specific high-affinity hERG blockers (e.g., E-4031) can rescue this mutant phenotype, but the exact mechanism is unknown. This study used accelerated molecular dynamics simulations to investigate how these mutations affect the hERG channel's structure, folding, endoplasmic reticulum (ER) retention, and trafficking. We reveal that these mutations induce structural changes in the channel, narrowing its central pore and altering the conformation of the intracellular domains. These changes expose internalization signals that contribute to ER retention and degradation of the mutant hERG channels. Moreover, the study found that the trafficking rescue drug E-4031 can inhibit these structural changes, potentially rescuing the mutant channels. This research offers valuable insights into the structural issues responsible for the degradation of rescuable transmembrane trafficking mutants. Understanding the defective trafficking structure of the hERG channel could help identify binding sites for small molecules capable of restoring proper folding and facilitating channel trafficking. This knowledge has the potential to lead to mechanism-based therapies that address the condition at the cellular level, which may prove more effective than treating clinical symptoms, ultimately offering hope for individuals with hereditary Long QT Syndrome.
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Affiliation(s)
| | | | - Khaled H. Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
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15
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Tarrat N, Schön JC, Cortés J. Dependence of lactose adsorption on the exposed crystal facets of metals: a comparative study of gold, silver and copper. Phys Chem Chem Phys 2024; 26:21134-21146. [PMID: 39069955 DOI: 10.1039/d4cp01559b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
In this theoretical work, we investigated the adsorption of a lactose molecule on metal-based surfaces, with a focus on the influence of the nature of the metal and of the type of exposed crystal facet on the adsorbed structures and energetics. More precisely, we considered three flat crystallographic facets of three face-centered cubic metals (gold, silver, and copper). For the global exploration of the energy landscape, we employed a multi-stage procedure where high-throughput searches, using a stochastic method that performs global optimization by iterating local searches, are followed by a refinement of the most probable adsorption conformations of the molecule at the ab initio level. We predicted the optimal conformation of lactose on each of the nine metal-surface combinations, classified the many low-energy minima into possible adsorption modes, and analyzed the structural, electronic and energetic aspects of the lactose molecule on the surface, as well as their dependence on the type of metal and exposed crystal facet. We observed structural similarities between the various minimum-energy conformations of lactose in vacuum and on the surface, a rough correlation between adsorption and interaction energies of the molecule, and a small charge transfer between molecule and surface whose direction is metal-dependent. During adsorption, an electronic reorganization occurs at the metal-molecule interface only, without affecting the vacuum-pointing atoms of the lactose molecule. For all types of surfaces, lactose exhibits the weakest adsorption on silver substrates, while for each coinage metal the adsorption is strongest on the (110) crystal facet. This study demonstrates that the control of exposed facets can allow to modulate the interaction between metals and small saccharides.
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Affiliation(s)
- Nathalie Tarrat
- CEMES, Université de Toulouse, CNRS, 29 rue Jeanne Marvig, 31055 Toulouse, France.
| | - J Christian Schön
- Max Planck Institute for Solid State Research, Heisenbergstr. 1, 70569 Stuttgart, Germany
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, 31400 Toulouse, France
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16
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Luo G, Li J, Qin X, Wang Q, Zhong J. Improved moisture barrier and mechanical properties of rice protein/sodium alginate films for banana and oil preservation: Effect of the type and addition form of fatty acid. Food Chem 2024; 460:140764. [PMID: 39121763 DOI: 10.1016/j.foodchem.2024.140764] [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: 12/09/2023] [Revised: 07/12/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024]
Abstract
Attenuating the moisture sensitivity of hydrophilic protein/polysaccharide-based films without impairing other properties remains a challenge. Fatty acid dispersed in Pickering emulsion was proposed to overcome such issue. An increase in fatty acid chain length slightly reduced the water vapor permeability (WVP) of emulsion films. As the number of fatty acid double bonds increased from 0 to 1, the WVP of emulsion films was significantly decreased by 14.02% while mechanical properties were significantly enhanced. More hydrogen bonds and stronger electrostatic interactions in the presence of fatty acids were observed by molecular dynamics simulation. The weight loss of bananas coated with oleic acid-incorporated film-forming emulsion was 6.81% lower than that of uncoated group after 4 days, and the corresponding film was more effective to delay oil oxidation than the commercial polypropylene film, indicating that the film is a promising alternative to food coating and packaging material.
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Affiliation(s)
- Guoliu Luo
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Jinsong Li
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Xiaoli Qin
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Qiang Wang
- Department of Biological and Chemical Engineering, Chongqing University of Education, Chongqing 400067, China.
| | - Jinfeng Zhong
- College of Food Science, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, China.
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17
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Briganti L, Manzine LR, de Mello Capetti CC, de Araújo EA, de Oliveira Arnoldi Pellegrini V, Guimaraes FEG, de Oliveira Neto M, Polikarpov I. Unravelling biochemical and structural features of Bacillus licheniformis GH5 mannanase using site-directed mutagenesis and high-resolution protein crystallography studies. Int J Biol Macromol 2024; 274:133182. [PMID: 38885857 DOI: 10.1016/j.ijbiomac.2024.133182] [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: 12/23/2023] [Revised: 05/20/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
Glycoside hydrolase family 5 (GH5) encompasses enzymes with several different activities, including endo-1,4-β-mannosidases. These enzymes are involved in mannan degradation, and have a number of biotechnological applications, such as mannooligosaccharide prebiotics production, stain removal and dyes decolorization, to name a few. Despite the importance of GH5 enzymes, only a few members of subfamily 7 were structurally characterized. In the present work, biochemical and structural characterization of Bacillus licheniformis GH5 mannanase, BlMan5_7 were performed and the enzyme cleavage pattern was analyzed, showing that BlMan5_7 requires at least 5 occupied subsites to perform efficient hydrolysis. Additionally, crystallographic structure at 1.3 Å resolution was determined and mannoheptaose (M7) was docked into the active site to investigate the interactions between substrate and enzyme through molecular dynamic (MD) simulations, revealing the existence of a - 4 subsite, which might explain the generation of mannotetraose (M4) as an enzyme product. Biotechnological application of the enzyme in stain removal was investigated, demonstrating that BlMan5_7 addition to washing solution greatly improves mannan-based stain elimination.
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Affiliation(s)
- Lorenzo Briganti
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil
| | - Livia R Manzine
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil
| | - Caio Cesar de Mello Capetti
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil
| | - Evandro Ares de Araújo
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials, Campinas 13083-970, São Paulo, Brazil
| | | | - Francisco Eduardo Gontijo Guimaraes
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil
| | - Mario de Oliveira Neto
- Departamento de Física e Biofísica, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Jr. s/n, Botucatu 18618-000, SP, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil.
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18
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Pang X, Han S, Zheng K, Jiang L, Wang J, Qian S. Cellulose nanocrystal-stabilized Pickering emulsion gels as vehicles for follicular delivery of minoxidil. Int J Biol Macromol 2024:134297. [PMID: 39097055 DOI: 10.1016/j.ijbiomac.2024.134297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 07/20/2024] [Accepted: 07/28/2024] [Indexed: 08/05/2024]
Abstract
Minoxidil (MXD) is the only topical over-the-counter medicine approved by the United States Food and Drug Administration for the treatment of androgenetic alopecia. For the purpose of targeting the delivery of MXD to dermal papilla in the hair follicle, MXD Pickering emulsion gels were fabricated based on the designability of deep eutectic solvent (DES) and the versatility of cellulose nanocrystal (CNC) and sodium carboxymethyl cellulose (CMC-Na). Structural studies and theoretical calculations results suggest that CNC can stabilize the interface between the MXD-DES and water, leading to the formation of Pickering emulsions. The rheological properties and stabilities of MXD Pickering emulsions were enhanced through gelation using CMC-Na, which highlights the good compatibility and effectiveness of natural polysaccharides in emulsion gels. Due to the particle size of emulsion droplets (679 nm) and the rheological properties of emulsion gel, the fabricated MXD formulations show in vivo hair regrowth promotion and hair follicle targeting capabilities. Interestingly, the MXD Pickering emulsion-based formulations exert therapeutic effects by upregulating the expression of hair growth factors. The proposed nanodrug strategy based on supramolecular strategies of CNC and CMC-Na provides an interesting avenue for androgenetic alopecia treatment.
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Affiliation(s)
- Xuan Pang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong 255049, China
| | - Song Han
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong 255049, China
| | - Kang Zheng
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong 255049, China.
| | - Liu Jiang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong 255049, China; School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, Shandong 255049, China.
| | - Jianping Wang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong 255049, China
| | - Shaosong Qian
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong 255049, China
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19
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Peiffer AL, Dugan AE, Kiessling LL. Soluble Human Lectins at the Host-Microbe Interface. Annu Rev Biochem 2024; 93:565-601. [PMID: 38640018 PMCID: PMC11296910 DOI: 10.1146/annurev-biochem-062917-012322] [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] [Indexed: 04/21/2024]
Abstract
Human lectins are integral to maintaining microbial homeostasis on the skin, in the blood, and at mucosal barriers. These proteins can recognize microbial glycans and inform the host about its microbial status. In accordance with their roles, their production can vary with tissue type. They also can have unique structural and biochemical properties, and they can influence microbial colonization at sites proximal and distal to their tissue of origin. In line with their classification as innate immune proteins, soluble lectins have long been studied in the context of acute infectious disease, but only recently have we begun to appreciate their roles in maintaining commensal microbial communities (i.e., the human microbiota). This review provides an overview of soluble lectins that operate at host-microbe interfaces, their glycan recognition properties, and their roles in physiological and pathological mechanisms.
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Affiliation(s)
- Amanda L Peiffer
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - A E Dugan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - L L Kiessling
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
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20
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Su P, Zhu X, Wilson SM, Feng Y, Samayoa-Oviedo HY, Sonnendecker C, Smith AJ, Zimmermann W, Laskin J. The effect of host size on binding in host-guest complexes of cyclodextrins and polyoxometalates. Chem Sci 2024; 15:11825-11836. [PMID: 39092096 PMCID: PMC11290418 DOI: 10.1039/d4sc01061b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/07/2024] [Indexed: 08/04/2024] Open
Abstract
Harnessing flexible host cavities opens opportunities for the design of novel supramolecular architectures that accommodate nanosized guests. This research examines unprecedented gas-phase structures of Keggin-type polyoxometalate PW12O40 3- (WPOM) and cyclodextrins (X-CD, X = α, β, γ, δ, ε, ζ) including previously unexplored large, flexible CDs. Using ion mobility spectrometry coupled to mass spectrometry (IM-MS) in conjunction with molecular dynamics (MD) simulations, we provide first insights into the binding modes between WPOM and larger CD hosts as isolated structures. Notably, γ-CD forms two distinct structures with WPOM through binding to its primary and secondary faces. We also demonstrate that ε-CD forms a deep inclusion complex, which encapsulates WPOM within its annular inner cavity. In contrast, ζ-CD adopts a saddle-like conformation in its complex with WPOM, which resembles its free form in solution. More intriguingly, the gas-phase CD-WPOM structures are highly correlated with their counterparts in solution as characterized by nuclear magnetic resonance (NMR) spectroscopy. The strong correlation between the gas- and solution phase structures of CD-WPOM complexes highlight the power of gas-phase IM-MS for the structural characterization of supramolecular complexes with nanosized guests, which may be difficult to examine using conventional approaches.
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Affiliation(s)
- Pei Su
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette Indiana 47907 USA
- Department of Chemistry, Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Xiao Zhu
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette Indiana 47907 USA
- Rosen Center for Advanced Computing, Purdue University West Lafayette Indiana 47907 USA
| | - Solita M Wilson
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette Indiana 47907 USA
| | - Yuanning Feng
- Department of Chemistry, Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
- Department of Chemistry and Biochemistry, The University of Oklahoma 101 Stephenson Parkway Norman Oklahoma 73019 USA
| | - Hugo Y Samayoa-Oviedo
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette Indiana 47907 USA
| | - Christian Sonnendecker
- Institute of Analytical Chemistry, Universität Leipzig Johannisallee 29 Leipzig 04103 Germany
| | - Andrew J Smith
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette Indiana 47907 USA
| | - Wolfgang Zimmermann
- Institute of Analytical Chemistry, Universität Leipzig Johannisallee 29 Leipzig 04103 Germany
| | - Julia Laskin
- Department of Chemistry, Purdue University 560 Oval Drive West Lafayette Indiana 47907 USA
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21
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Yasuda N, Ali S, Aman A, Krusong K, Herfindo N, Chavasiri W, Choowongkomon K, Wolschann P, Mahalapbutr P, Rungrotmongkol T, Hannongbua S. In vitro and in silico studies of the inclusion complexation of 8-bromobaicalein with β-cyclodextrins. J Mol Graph Model 2024; 132:108840. [PMID: 39128382 DOI: 10.1016/j.jmgm.2024.108840] [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: 05/18/2024] [Revised: 07/29/2024] [Accepted: 07/29/2024] [Indexed: 08/13/2024]
Abstract
Baicalein, a flavone derived from Scutellaria baicalensis Georgi, exhibits potent anti-inflammatory, antiviral, and anticancer properties. Its derivative, known as 8-bromobaicalein (BB), has been found to have strong cytotoxic effect on MCF-7 human breast cancer cells. However, its limited solubility in water has hindered its potential for wider applications. To address this issue, we investigated the use of cyclodextrins specifically βCD, 2,6-di-O-methyl-β-cyclodextrin (DMβCD), and hydroxypropyl-β-cyclodextrin (HPβCD) to improve the solubility of BB through inclusion complexation. During 250 ns molecular dynamics simulations, it was found that BB can form inclusion complexes with all βCDs. These complexes exhibit two distinct orientations: chromone group insertion (C-form) and phenyl group insertion (P-form). The formation of these complexes is primarily driven by van der Waals interactions. DMβCD has the highest number of atom contacts with BB and the lowest solvent accessibility in the hydrophobic cavity. These results coincide with the highest binding affinity from the MM/GBSA-based free energy calculation method. Experimental phase solubility diagrams revealed a 1:1 stoichiometric ratio (AL type) between BB and βCDs, in which BB/DMβCD showed the highest stability. The formation of inclusion complexes was confirmed by differential scanning calorimetry and scanning electron microscope methods. Additionally, the BB/DMβCD inclusion complex demonstrated significantly higher anticancer activity against MCF-7 human breast cancer cells compared to BB alone. These findings underscore the potential of DMβCD for formulating BB in pharmaceutical and medical applications.
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Affiliation(s)
- Noriyuki Yasuda
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Saba Ali
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Aamir Aman
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kuakarun Krusong
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Noval Herfindo
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Warinthorn Chavasiri
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Peter Wolschann
- Institute of Theoretical Chemistry, University of Vienna, 1090, Vienna, Austria
| | - Panupong Mahalapbutr
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
| | - Thanyada Rungrotmongkol
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand; Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Supot Hannongbua
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
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22
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Xu Z, Zhang H, Tian J, Ku X, Wei R, Hou J, Zhang C, Yang F, Zou X, Li Y, Kaji H, Tao SC, Kuno A, Yan W, Da LT, Zhang Y. O-glycosylation of SARS-CoV-2 spike protein by host O-glycosyltransferase strengthens its trimeric structure. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39066577 DOI: 10.3724/abbs.2024127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024] Open
Abstract
Protein O-glycosylation, also known as mucin-type O-glycosylation, is one of the most abundant glycosylation in mammalian cells. It is initially catalyzed by a family of polypeptide GalNAc transferases (ppGalNAc-Ts). The trimeric spike protein (S) of SARS-CoV-2 is highly glycosylated and facilitates the virus's entry into host cells and membrane fusion of the virus. However, the functions and relationship between host ppGalNAc-Ts and O-glycosylation on the S protein remain unclear. Herein, we identify 15 O-glycosites and 10 distinct O-glycan structures on the S protein using an HCD-product-dependent triggered ETD mass spectrometric analysis. We observe that the isoenzyme T6 of ppGalNAc-Ts (ppGalNAc-T6) exhibits high O-glycosylation activity for the S protein, as demonstrated by an on-chip catalytic assay. Overexpression of ppGalNAc-T6 in HEK293 cells significantly enhances the O-glycosylation level of the S protein, not only by adding new O-glycosites but also by increasing O-glycan heterogeneity. Molecular dynamics simulations reveal that O-glycosylation on the protomer-interface regions, modified by ppGalNAc-T6, potentially stabilizes the trimeric S protein structure by establishing hydrogen bonds and non-polar interactions between adjacent protomers. Furthermore, mutation frequency analysis indicates that most O-glycosites of the S protein are conserved during the evolution of SARS-CoV-2 variants. Taken together, our finding demonstrate that host O-glycosyltransferases dynamically regulate the O-glycosylation of the S protein, which may influence the trimeric structural stability of the protein. This work provides structural insights into the functional role of specific host O-glycosyltransferases in regulating the O-glycosylation of viral envelope proteins.
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Affiliation(s)
- Zhijue Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
- SCSB (China)-AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai 200240, China
| | - Han Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiaqi Tian
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Medical Information and Engineering, Xuzhou Medical University, Xuzhou 221000, China
| | - Xin Ku
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rumeng Wei
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingli Hou
- Intrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Can Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fang Yang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xia Zou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Li
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hiroyuki Kaji
- SCSB (China)-AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai 200240, China
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Atsushi Kuno
- SCSB (China)-AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai 200240, China
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8577, Japan
| | - Wei Yan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
- SCSB (China)-AIST (Japan) Joint Medical Glycomics Laboratory, Shanghai 200240, China
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23
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Rao D, Zhu L, Liu W, Guo Z. Molecular Mechanism of Double-Displacement Retaining β-Kdo Glycosyltransferase WbbB. J Phys Chem B 2024. [PMID: 39051443 DOI: 10.1021/acs.jpcb.4c02073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Glycosyltransferases (GTs) are pivotal enzymes involved in glycosidic bond synthesis, which can lead to either retention or inversion of the glycosyl moiety's anomeric configuration. However, the catalytic mechanism for retaining GTs remains a subject of controversy. In this study, we employ MD and QM/MM metadynamics to investigate the double-displacement catalytic mechanism of the retaining β-Kdo transferase WbbB. Our findings demonstrate that the nucleophile Asp232 initiates the reaction by attacking the sugar ring containing a carboxylate at the anomeric position, forming a covalent adduct. Subsequently, the adduct undergoes a rotational rearrangement, ensuring proper orientation of the anomeric carbon for the acceptor substrate. In the second step, Glu158 acts as the catalytic base to abstract the proton of the acceptor substrate to complete the transglycosylation reaction. Notably, His265 does not function as the anticipated catalytic acid; instead, it stabilizes the phosphate group through H-bonding interactions. Our simulations support the double-displacement mechanism implicated from the crystallographic studies of WbbB. This mechanism deviates from the common SNi-type and retaining glycoside hydrolase mechanisms, thereby expanding our understanding of GT catalytic mechanisms.
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Affiliation(s)
- Deming Rao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Lin Zhu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Weiqiong Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Zhiyong Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
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24
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Pietrafesa D, Napoli A, Iacovelli F, Romeo A, Tucci FG, Billi D, Falconi M. Deciphering the Role of Trehalose in Chroococcidiopsis sp. 029's High-Desiccation Resistance: Sequence Determination, Structural Modelling and Simulative Analysis of the 30S Ribosomal Subunit. Molecules 2024; 29:3486. [PMID: 39124891 PMCID: PMC11314286 DOI: 10.3390/molecules29153486] [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: 05/15/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
Desert strains of the genus Chroococcidiopsis are among the most desiccation-resistant cyanobacteria capable of anhydrobiosis. The accumulation of two sugars, sucrose and trehalose, facilitates the entrance of anhydrobiotes into a reversible state of dormancy by stabilizing cellular components upon water removal. This study aimed to evaluate, at the atomistic level, the role of trehalose in desiccation resistance by using as a model system the 30S ribosomal subunit of the desert cyanobacterium Chroococcidiopsis sp. 029. Molecular dynamic simulations provided atomistic evidence regarding its protective role on the 30S molecular structure. Trehalose forms an enveloping shell around the ribosomal subunit and stabilizes the structures through a network of direct interactions. The simulation confirmed that trehalose actively interacts with the 30S ribosomal subunit and that, by replacing water molecules, it ensures ribosomal structural integrity during desiccation, thus enabling protein synthesis to be carried out upon rehydration.
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Affiliation(s)
| | | | | | | | | | | | - Mattia Falconi
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (D.P.); (A.N.); (F.I.); (A.R.); (F.G.T.); (D.B.)
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25
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Lutsyk V, Wolski P, Plazinski W. The Conformation of Glycosidic Linkages According to Various Force Fields: Monte Carlo Modeling of Polysaccharides Based on Extrapolation of Short-Chain Properties. J Chem Theory Comput 2024; 20:6350-6368. [PMID: 38985993 PMCID: PMC11270825 DOI: 10.1021/acs.jctc.4c00543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024]
Abstract
The conformational features of the glycosidic linkage are the most important variable to consider when studying di-, oligo-, and polysaccharide molecules using molecular dynamics (MD) simulations. The accuracy of the theoretical model describing this degree of freedom influences the quality of the results obtained from MD calculations based on this model. This article focuses on the following two issues related to the conformation of the glycosidic linkage. First, we describe the results of a comparative analysis of the predictions of three carbohydrate-dedicated classical force fields for MD simulations, namely, CHARMM, GLYCAM, and GROMOS, in the context of different parameters of structural and energetic nature related to the conformation of selected types of glycosidic linkages, α(1 → 4), β(1 → 3), and β(1 → 4), connecting glucopyranose units. This analysis revealed several differences, mainly concerning the energy levels of the secondary and tertiary conformers and the linkage flexibility within the dominant exo-syn conformation for α(1 → 4) and β(1 → 3) linkages. Some aspects of the comparative analysis also included the newly developed, carbohydrate-dedicated Martini 3 coarse-grained force field. Second, to overcome the time-scale problem associated with sampling slow degrees of freedom in polysaccharide chains during MD simulations, we developed a coarse-grained (CG) model based on the data from MD simulations and designed for Monte Carlo modeling. This model (CG MC) is based on information from simulations of short saccharide chains, effectively sampled in atomistic MD simulations, and is capable of extrapolating local conformational properties to the case of polysaccharides of arbitrary length. The CG MC model has the potential to estimate the conformations of very long polysaccharide chains, taking into account the influence of secondary and tertiary conformations of glycosidic linkages. With respect to the comparative analysis of force fields, the application of CG MC modeling showed that relatively small differences in the predictions of individual force fields with respect to a single glycosidic linkage accumulate when considering their effect on the structure of longer chains, leading to drastically different predictions with respect to parameters describing the polymer conformation, such as the persistence length.
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Affiliation(s)
- Valery Lutsyk
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Pawel Wolski
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Wojciech Plazinski
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
- Department
of Biopharmacy, Medical University of Lublin, Chodzki 4a, 20-093 Lublin, Poland
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26
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Wan J, Luo C. Accumulation of Hydrogen Bonds and van der Waals Interactions Determines Force Response between Two Parallel Cellulose Chains: Steered Molecular Dynamics Simulations. J Phys Chem B 2024; 128:6742-6750. [PMID: 38975805 DOI: 10.1021/acs.jpcb.4c01826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
We investigated the response forces between two parallel cellulose chains during the shearing and tearing processes by using steered molecular dynamics simulations. It was found that there are two logarithmic dependencies between response force and pulling speed in shearing processes but only one in tearing, according to Bell's equation by fitting the f-ln v curve. The mechanism is that there are 2-fold interactions determining the force response between two parallel cellulose chains resisting chain separation during a shearing process. Our results indicate that hydrogen bonds dominate the interchain interactions in the fast pull mode (FPM) for shearing, while van der Waals interactions dominate in the slow pull mode (SPM). For tearing, the one-by-one breaking of hydrogen bonds and van der Waals interactions plays a main role.
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Affiliation(s)
- Jia Wan
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Chuanfu Luo
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
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27
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Mészáros Z, Kulik N, Petrásková L, Bojarová P, Texidó M, Planas A, Křen V, Slámová K. Three-Step Enzymatic Remodeling of Chitin into Bioactive Chitooligomers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15613-15623. [PMID: 38978453 PMCID: PMC11261597 DOI: 10.1021/acs.jafc.4c03077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024]
Abstract
Here we describe a complex enzymatic approach to the efficient transformation of abundant waste chitin, a byproduct of the food industry, into valuable chitooligomers with a degree of polymerization (DP) ranging from 6 to 11. This method involves a three-step process: initial hydrolysis of chitin using engineered variants of a novel fungal chitinase from Talaromyces flavus to generate low-DP chitooligomers, followed by an extension to the desired DP using the high-yielding Y445N variant of β-N-acetylhexosaminidase from Aspergillus oryzae, achieving yields of up to 57%. Subsequently, enzymatic deacetylation of chitooligomers with DP 6 and 7 was accomplished using peptidoglycan deacetylase from Bacillus subtilis BsPdaC. The innovative enzymatic procedure demonstrates a sustainable and feasible route for converting waste chitin into unavailable bioactive chitooligomers potentially applicable as natural pesticides in ecological and sustainable agriculture.
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Affiliation(s)
- Zuzana Mészáros
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Natalia Kulik
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Lucie Petrásková
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Pavla Bojarová
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Mònica Texidó
- Laboratory
of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, ES 08017 Barcelona, Spain
| | - Antoni Planas
- Laboratory
of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, ES 08017 Barcelona, Spain
| | - Vladimír Křen
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Kristýna Slámová
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
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28
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Goode-Romero G, Dominguez L. Descriptive molecular pharmacology of the δ opioid receptor (DOR): A computational study with structural approach. PLoS One 2024; 19:e0304068. [PMID: 38991032 PMCID: PMC11239112 DOI: 10.1371/journal.pone.0304068] [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: 09/07/2023] [Accepted: 05/06/2024] [Indexed: 07/13/2024] Open
Abstract
This work focuses on the δ receptor (DOR), a G protein-coupled receptor (GPCR) belonging to the opioid receptor group. DOR is expressed in numerous tissues, particularly within the nervous system. Our study explores computationally the receptor's interactions with various ligands, including opiates and opioid peptides. It elucidates how these interactions influence the δ receptor response, relevant in a wide range of health and pathological processes. Thus, our investigation aims to explore the significance of DOR as an incoming drug target for pain relief and neurodegenerative diseases and as a source for novel opioid non-narcotic analgesic alternatives. We analyze the receptor's structural properties and interactions using Molecular Dynamics (MD) simulations and Gaussian-accelerated MD across different functional states. To thoroughly assess the primary differences in the structural and conformational ensembles across our different simulated systems, we initiated our study with 1 μs of conventional Molecular Dynamics. The strategy was chosen to encompass the full activation cycle of GPCRs, as activation processes typically occur within this microsecond range. Following the cMD, we extended our study with an additional 100 ns of Gaussian accelerated Molecular Dynamics (GaMD) to enhance the sampling of conformational states. This simulation approach allowed us to capture a comprehensive range of dynamic interactions and conformational changes that are crucial for GPCR activation as influenced by different ligands. Our study includes comparing agonist and antagonist complexes to uncover the collective patterns of their functional states, regarding activation, blocking, and inactivation of DOR, starting from experimental data. In addition, we also explored interactions between agonist and antagonist molecules from opiate and opioid classifications to establish robust structure-activity relationships. These interactions have been systematically quantified using a Quantitative Structure-Activity Relationships (QSAR) model. This research significantly contributes to our understanding of this significant pharmacological target, which is emerging as an attractive subject for drug development.
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Affiliation(s)
- Guillermo Goode-Romero
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura Dominguez
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
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29
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Boushehri S, Holey H, Brosz M, Gumbsch P, Pastewka L, Aponte-Santamaría C, Gräter F. O-glycans Expand Lubricin and Attenuate Its Viscosity and Shear Thinning. Biomacromolecules 2024; 25:3893-3908. [PMID: 38815979 PMCID: PMC11238335 DOI: 10.1021/acs.biomac.3c01348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 06/01/2024]
Abstract
Lubricin, an intrinsically disordered glycoprotein, plays a pivotal role in facilitating smooth movement and ensuring the enduring functionality of synovial joints. The central domain of this protein serves as a source of this excellent lubrication and is characterized by its highly glycosylated, negatively charged, and disordered structure. However, the influence of O-glycans on the viscosity of lubricin remains unclear. In this study, we employ molecular dynamics simulations in the absence and presence of shear, along with continuum simulations, to elucidate the intricate interplay between O-glycans and lubricin and the impact of O-glycans on lubricin's conformational properties and viscosity. We found the presence of O-glycans to induce a more extended conformation in fragments of the disordered region of lubricin. These O-glycans contribute to a reduction in solution viscosity but at the same time weaken shear thinning at high shear rates, compared to nonglycosylated systems with the same density. This effect is attributed to the steric and electrostatic repulsion between the fragments, which prevents their conglomeration and structuring. Our computational study yields a mechanistic mechanism underlying previous experimental observations of lubricin and paves the way to a more rational understanding of its function in the synovial fluid.
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Affiliation(s)
- Saber Boushehri
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany
- University of Heidelberg, Im Neuenheimer Feld 205, Heidelberg 69120, Germany
- Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
| | - Hannes Holey
- Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
- Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, Freiburg 79110, Germany
| | - Matthias Brosz
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany
- University of Heidelberg, Im Neuenheimer Feld 205, Heidelberg 69120, Germany
| | - Peter Gumbsch
- Karlsruhe Institute of Technology (KIT), Karlsruhe 76131, Germany
- Fraunhofer IWM, Wöhlerstraße 11, Freiburg 79108, Germany
| | - Lars Pastewka
- Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, Freiburg 79110, Germany
| | - Camilo Aponte-Santamaría
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany
- University of Heidelberg, Im Neuenheimer Feld 205, Heidelberg 69120, Germany
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30
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Mikaelian G, Megariotis G, Theodorou DN. Interactions of a Novel Anthracycline with Oligonucleotide DNA and Cyclodextrins in an Aqueous Environment. J Phys Chem B 2024; 128:6291-6307. [PMID: 38899795 PMCID: PMC11228990 DOI: 10.1021/acs.jpcb.4c02213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
Berubicin, a chemotherapy medication belonging to the class of anthracyclines, is simulated in double-stranded DNA sequences and cyclodextrins in an aqueous environment via full-atom molecular dynamics simulations on the time scale of microseconds. The drug is studied in both the neutral and protonated states so as to better comprehend the role of its charge in the formed complexes. The noncovalent berubicin-DNA and berubicin-cyclodextrin complexes are investigated in detail, paying special attention to their thermodynamic description by employing the double decoupling method, the solvent balance method, the weighted solvent accessible surface model, and the linear interaction energy method. A novel approach for extracting the desolvation thermodynamics of the binding process is also presented. Both the binding and desolvation Gibbs energies are decomposed into entropic and enthalpic contributions so as to elucidate the nature of complexation and its driving forces. Selected structural and geometrical properties of all the complexes, which are all stable, are analyzed. Both cyclodextrins under consideration are widely utilized for drug delivery purposes, and a comparative investigation between their bound states with berubicin is carried out.
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Affiliation(s)
- Georgios Mikaelian
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
| | - Grigorios Megariotis
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
- School
of Engineering, Department of Mineral Resources Engineering, University of Western Macedonia, 50100 Kozani, Greece
| | - Doros N. Theodorou
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
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31
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Meredith R, Zhu Y, Yoon MK, Tetrault T, Lin J, Zhang W, McGurn M, Cook E, Popp R, Shit P, Carmichael I, Serianni AS. Methyl α-D-galactopyranosyl-(1→3)-β-D-galactopyranoside and methyl β-D-galactopyranosyl-(1→3)-β-D-galactopyranoside: Glycosidic linkage conformation determined from MA'AT analysis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:544-555. [PMID: 38414300 DOI: 10.1002/mrc.5424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 02/29/2024]
Abstract
MA'AT analysis has been applied to two biologically-important O-glycosidic linkages in two disaccharides, α-D-Galp-(1→3)-β-D-GalpOMe (3) and β-D-Galp-(1→3)-β-D-GalpOMe (4). Using density functional theory (DFT) to obtain parameterized equations relating a group of trans-O-glycosidic NMR spin-couplings to either phi (ϕ') or psi (ψ'), and experimental 3JCOCH, 2JCOC, and 3JCOCC spin-couplings measured in aqueous solution in 13C-labeled isotopomers, probability distributions of ϕ' and ψ' in each linkage were determined and compared to those determined by aqueous 1-μs molecular dynamics (MD) simulation. Good agreement was found between the MA'AT and single-state MD conformational models of these linkages for the most part, with modest (approximately <15°) differences in the mean values of ϕ' and ψ', although the envelope of allowed angles (encoded in circular standard deviations or CSDs) is consistently larger for ϕ' determined from MA'AT analysis than from MD for both linkages. The MA'AT model of the α-Galp-(1→3)-β-Galp linkage agrees well with those determined previously using conventional NMR methods (3JCOCH values and/or 1H-1H NOEs), but some discrepancy was observed for the β-Galp-(1→3)-β-Galp linkage, which may arise from errors in the conventions used to describe the linkage torsion angles. Statistical analyses of X-ray crystal structures show ranges of ϕ' and ψ' for both linkages that include the mean angles determined from MA'AT analyses, although both angles adopt a wide range of values in the crystalline state, with ϕ' in β-Galp-(1→3)-β-Galp linkages showing greater-than-expected conformational variability.
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Affiliation(s)
- Reagan Meredith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Yuping Zhu
- Discovery Chemistry, Merck Research Laboratories, Kenilworth, New Jersey, USA
| | - Mi-Kyung Yoon
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Timothy Tetrault
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jieye Lin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Wenhui Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Margaret McGurn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Evan Cook
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Reed Popp
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Pradip Shit
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Ian Carmichael
- Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana, USA
| | - Anthony S Serianni
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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32
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Urban J, Jin C, Thomsson KA, Karlsson NG, Ives CM, Fadda E, Bojar D. Predicting glycan structure from tandem mass spectrometry via deep learning. Nat Methods 2024; 21:1206-1215. [PMID: 38951670 PMCID: PMC11239490 DOI: 10.1038/s41592-024-02314-6] [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: 06/13/2023] [Accepted: 05/17/2024] [Indexed: 07/03/2024]
Abstract
Glycans constitute the most complicated post-translational modification, modulating protein activity in health and disease. However, structural annotation from tandem mass spectrometry (MS/MS) data is a bottleneck in glycomics, preventing high-throughput endeavors and relegating glycomics to a few experts. Trained on a newly curated set of 500,000 annotated MS/MS spectra, here we present CandyCrunch, a dilated residual neural network predicting glycan structure from raw liquid chromatography-MS/MS data in seconds (top-1 accuracy: 90.3%). We developed an open-access Python-based workflow of raw data conversion and prediction, followed by automated curation and fragment annotation, with predictions recapitulating and extending expert annotation. We demonstrate that this can be used for de novo annotation, diagnostic fragment identification and high-throughput glycomics. For maximum impact, this entire pipeline is tightly interlaced with our glycowork platform and can be easily tested at https://colab.research.google.com/github/BojarLab/CandyCrunch/blob/main/CandyCrunch.ipynb . We envision CandyCrunch to democratize structural glycomics and the elucidation of biological roles of glycans.
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Affiliation(s)
- James Urban
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Chunsheng Jin
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kristina A Thomsson
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Niclas G Karlsson
- Section of Pharmacy, Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway
| | - Callum M Ives
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Elisa Fadda
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Daniel Bojar
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.
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33
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Hu X, Liu L, Zhong J, Liu X, Qin X. Improved physicochemical properties and in vitro digestion of walnut oil microcapsules with soy protein isolate and highly oxidized konjac glucomannan as wall materials. Food Chem 2024; 444:138640. [PMID: 38325078 DOI: 10.1016/j.foodchem.2024.138640] [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: 07/30/2023] [Revised: 01/18/2024] [Accepted: 01/29/2024] [Indexed: 02/09/2024]
Abstract
This study investigated the effect of the oxidation degrees of oxidized konjac glucomannan (OKGM) on the encapsulation efficiency (EE), physicochemical and in vitro digestive properties of soy protein isolate (SPI)-based microcapsules walnut oil using experimental and computational approaches. Microcapsules had the highest EE when the ratio of OKGM and SPI to oil was 2.5:1. With increasing the oxidation degree of OKGM, the EE of microcapsules was increased and the hygroscopicity was decreased. Molecular dynamics simulation results showed that SPI/oil/highly OKGM had relatively low binding energy (-4.03 × 106 kJ/mol) and strong electrostatic interactions, which may contribute to a higher EE and lower hygroscopicity of microcapsules, respectively. The oxidative stability of the oil was markedly improved by SPI and OKGM, and microcapsules prepared with SPI and highly OKGM had the highest in vitro digestion. This study provided theoretical support for broadening the application of microcapsules prepared with SPI and OKGM.
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Affiliation(s)
- Xiao Hu
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Lu Liu
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Jinfeng Zhong
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Xiong Liu
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Xiaoli Qin
- College of Food Science, Southwest University, Chongqing 400715, China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, China.
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34
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Nepravishta R, Ramírez-Cárdenas J, Rocha G, Walpole S, Hicks T, Monaco S, Muñoz-García JC, Angulo J. Fast Quantitative Validation of 3D Models of Low-Affinity Protein-Ligand Complexes by STD NMR Spectroscopy. J Med Chem 2024; 67:10025-10034. [PMID: 38848103 PMCID: PMC11215723 DOI: 10.1021/acs.jmedchem.4c00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/26/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024]
Abstract
Low-affinity protein-ligand interactions are important for many biological processes, including cell communication, signal transduction, and immune responses. Structural characterization of these complexes is also critical for the development of new drugs through fragment-based drug discovery (FBDD), but it is challenging due to the low affinity of fragments for the binding site. Saturation transfer difference (STD) NMR spectroscopy has revolutionized the study of low-affinity receptor-ligand interactions enabling binding detection and structural characterization. Comparison of relaxation and exchange matrix calculations with 1H STD NMR experimental data is essential for the validation of 3D structures of protein-ligand complexes. In this work, we present a new approach based on the calculation of a reduced relaxation matrix, in combination with funnel metadynamics MD simulations, that allows a very fast generation of experimentally STD-NMR-validated 3D structures of low-affinity protein-ligand complexes.
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Affiliation(s)
- Ridvan Nepravishta
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
- Cancer Research Horizons, CRUK Scotland Institute, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, U.K
| | - Jonathan Ramírez-Cárdenas
- Institute for Chemical Research (IIQ), CSIC - University of Seville, 49 Américo Vespucio, 41092 Seville, Spain
| | - Gabriel Rocha
- Institute for Chemical Research (IIQ), CSIC - University of Seville, 49 Américo Vespucio, 41092 Seville, Spain
| | - Samuel Walpole
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Thomas Hicks
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Juan C Muñoz-García
- Institute for Chemical Research (IIQ), CSIC - University of Seville, 49 Américo Vespucio, 41092 Seville, Spain
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
- Institute for Chemical Research (IIQ), CSIC - University of Seville, 49 Américo Vespucio, 41092 Seville, Spain
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35
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Toukach P. Carbohydrate Structure Database: current state and recent developments. Anal Bioanal Chem 2024:10.1007/s00216-024-05383-w. [PMID: 38914734 DOI: 10.1007/s00216-024-05383-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/18/2024] [Accepted: 05/28/2024] [Indexed: 06/26/2024]
Abstract
Carbohydrate Structure Database (CSDB) is a curated glycan data collection and a glycoinformatic platform. In this report, its database, analytical, and other components that have appeared for the recent years are reviewed. The major improvements were achieving close-to-full coverage on glycans from microorganisms, launching modules for glycosyltransferases and saccharide conformations, online glycan builder and 3D modeler, NMR simulator, NMR-based structure predictor, and other tools.
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Affiliation(s)
- Philip Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia.
- Faculty of Chemistry, National Research University Higher School of Economics, Moscow, Russia.
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36
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Ananya YK, Ramya L. Deciphering the conformational dynamics of Myelin Oligodendrocyte glycoprotein in the myelin sheath. J Biomol Struct Dyn 2024:1-8. [PMID: 38910432 DOI: 10.1080/07391102.2024.2337956] [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: 06/13/2023] [Accepted: 03/25/2024] [Indexed: 06/25/2024]
Abstract
Myelin Oligodendrocyte Glycoprotein (MOG) is a transmembrane protein in the myelin sheath. It acts as an auto-antigen under certain unknown conditions causing demyelination, thus resulting in Myelin Oligodendrocyte Glycoprotein Antibody-associated Disease (MOGAD). The significance of glycosylation in the conformational dynamics of the extracellular region (EC1) of the MOG were evident from the previous computational studies. Here, in this study, we performed the molecular dynamics simulation of the entire human MOG in the myelin sheath for 100 ns using the NAMD program. The results indicated that the EC1 and cytoplasmic region (CP) dominate the conformational rigidity of the protein, and enhance its interaction with lipids. This in turn helps in maintaining the myelin integrity in the presence of glycan. The transmembrane regions have reduced interaction with lipids in the glycosylated system. Moreover, the C-terminal extracellular region 2 (EC2) behaves exactly opposite to that of EC1 in the glycan presence. This may be attributed to the glycosylation site in the EC1 region. Hence, not only the region EC1 (having 3 crucial epitopes) but even the CP region were important for understanding the proper function of MOG in the glycan presence.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Y K Ananya
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thirumalaisamudram, Thanjavur, Tamilnadu, India
| | - L Ramya
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thirumalaisamudram, Thanjavur, Tamilnadu, India
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37
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Hao D, Niu LN. Computational Study on the Wealth Conformations of Hepatitis C Virus Envelope Glycoprotein 2 and Role of Its Glycan Coat. J Chem Inf Model 2024; 64:4811-4821. [PMID: 38861660 DOI: 10.1021/acs.jcim.4c00521] [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: 06/13/2024]
Abstract
Hepatitis C virus (HCV) is a major cause of chronic liver disease and hepatocellular carcinoma. Antibody development efforts mainly revolve around HCV envelope glycoprotein 2 (E2), which mediates host cell entry by interacting with several cell surface receptors, including CD81. We still have limited knowledge about the structural ensembles and the dynamic behavior of both the CD81 binding sites and the glycans on E2. Here, multiple microsecond-long, all-atom molecular dynamics (MD) simulations, as well as a Markov state model (MSM), were performed to provide an atomistic perspective on the dynamic nature of E2 and its glycans. End-to-end accessibility analyses outline a complete overview of the vulnerabilities of the glycan shield of E2, which may be exploited in therapeutic efforts. Additionally, the Markov state model built from the simulation maps four metastable states for AS412 and three metastable states for the front layer in CD81 binding sites, while binding with HEPC3 would induce a conformation selection for both of them. Overall, this work presents hitherto unseen functional and structural insights into E2 and its glycan coat, providing a new theoretical foundation to control the conformational plasticity of E2 that could be harnessed for vaccine development.
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Affiliation(s)
- Dongxiao Hao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an 710032, China
- School of Electronics and Information Engineering, Ankang University, Ankang 725000, China
| | - Li-Na Niu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Diseases, Shaanxi Key Laboratory of Stomatology, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an 710032, China
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38
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Bagchi A, Stayrook SE, Xenaki KT, Starbird CA, Doulkeridou S, El Khoulati R, Roovers RC, Schmitz KR, van Bergen En Henegouwen PMP, Ferguson KM. Structural insights into the role and targeting of EGFRvIII. Structure 2024:S0969-2126(24)00195-3. [PMID: 38908376 DOI: 10.1016/j.str.2024.05.018] [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: 11/03/2023] [Revised: 04/06/2024] [Accepted: 05/28/2024] [Indexed: 06/24/2024]
Abstract
The epidermal growth factor receptor (EGFR) is a well-known oncogenic driver in lung and other cancers. In glioblastoma multiforme (GBM), the EGFR deletion variant III (EGFRvIII) is frequently found alongside EGFR amplification. Agents targeting the EGFR axis have shown limited clinical benefits in GBM and the role of EGFRvIII in GBM is poorly understood. To shed light on the role of EGFRvIII and its potential as a therapeutic target, we determined X-ray crystal structures of a monomeric EGFRvIII extracellular region (ECR). The EGFRvIII ECR resembles the unliganded conformation of EGFR, including the orientation of the C-terminal region of domain II. Domain II is mostly disordered, but the ECR structure is compact. We selected a nanobody with preferential binding to EGFRvIII relative to EGFR and structurally defined an epitope on domain IV that is occluded in the unliganded intact EGFR. These findings suggest new avenues for EGFRvIII targeting in GBM.
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Affiliation(s)
- Atrish Bagchi
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven E Stayrook
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Katerina T Xenaki
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Chrystal A Starbird
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA
| | - Sofia Doulkeridou
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Rachid El Khoulati
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Rob C Roovers
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Karl R Schmitz
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Paul M P van Bergen En Henegouwen
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Science Faculty, Utrecht University, Utrecht 3584CH, the Netherlands
| | - Kathryn M Ferguson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT 06516, USA.
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39
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Stanevich V, Oyeniran O, Somani S. Modeling Chromatography Binding through Molecular Dynamics Simulations with Resin Fragments. J Phys Chem B 2024; 128:5557-5566. [PMID: 38809811 PMCID: PMC11181327 DOI: 10.1021/acs.jpcb.4c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 05/31/2024]
Abstract
Accurate atomistic modeling of the interactions of a chromatography resin with a solute can inform the selection of purification conditions for a product, an important problem in the biotech and pharmaceutical industries. We present a molecular dynamics simulation-based approach for the qualitative prediction of interaction sites (specificity) and retention times (affinity) of a protein for a given chromatography resin. We mimicked the resin with an unrestrained ligand composed of the resin headgroup coupled with successively larger fragments of the agarose backbone. The interactions of the ligand with the protein are simulated in an explicit solvent using the Replica Exchange Molecular Dynamics enhanced sampling approach in conjunction with Hydrogen Mass Repartitioning (REMD-HMR). We computed the ligand interaction surface from the simulation trajectories and correlated the features of the interaction surface with experimentally determined retention times. The simulation and analysis protocol were first applied to a series of ubiquitin mutants for which retention times on Capto MMC resin are available. The ubiquitin simulations helped identify the optimal ligand that was used in subsequent simulations on six proteins for which Capto MMC elution times are available. For each of the six proteins, we computed the interaction surface and characterized it in terms of a range of simulation-averaged residue-level physicochemical descriptors. Modeling of the salt concentrations required for elution with respect to the descriptors resulted in a linear fit in terms of aromaphilicity and Kyte-Doolittle hydrophobicity that was robust to outliers, showed high correlation, and correctly ranked the protein elution order. The physics-based model building approach described here does not require a large experimental data set and can be readily applied to different resins and diverse biomolecules.
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Affiliation(s)
- Vitali Stanevich
- Protein
Therapeutics API Development, Janssen Research & Development,
LLC, a Johnson & Johnson company, Malvern, Pennsylvania 19355, United States
| | - Oluyemi Oyeniran
- Statistics
and Decision Sciences, Janssen Research & Development, LLC, a Johnson & Johnson company, Spring House, Pennsylvania 19002, United States
| | - Sandeep Somani
- In Silico
Discovery, Janssen Research & Development, LLC, a Johnson & Johnson company, Spring House, Pennsylvania 19002, United States
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40
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Bagdonaite I, Abdurahman S, Mirandola M, Pasqual D, Frank M, Narimatsu Y, Joshi HJ, Vakhrushev SY, Salata C, Mirazimi A, Wandall HH. Targeting host O-linked glycan biosynthesis affects Ebola virus replication efficiency and reveals differential GalNAc-T acceptor site preferences on the Ebola virus glycoprotein. J Virol 2024; 98:e0052424. [PMID: 38757972 PMCID: PMC11237518 DOI: 10.1128/jvi.00524-24] [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: 03/21/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Ebola virus glycoprotein (EBOV GP) is one of the most heavily O-glycosylated viral glycoproteins, yet we still lack a fundamental understanding of the structure of its large O-glycosylated mucin-like domain and to what degree the host O-glycosylation capacity influences EBOV replication. Using tandem mass spectrometry, we identified 47 O-glycosites on EBOV GP and found similar glycosylation signatures on virus-like particle- and cell lysate-derived GP. Furthermore, we performed quantitative differential O-glycoproteomics on proteins produced in wild-type HEK293 cells and cell lines ablated for the three key initiators of O-linked glycosylation, GalNAc-T1, -T2, and -T3. The data show that 12 out of the 47 O-glycosylated sites were regulated, predominantly by GalNAc-T1. Using the glycoengineered cell lines for authentic EBOV propagation, we demonstrate the importance of O-linked glycan initiation and elongation for the production of viral particles and the titers of progeny virus. The mapped O-glycan positions and structures allowed to generate molecular dynamics simulations probing the largely unknown spatial arrangements of the mucin-like domain. The data highlight targeting GALNT1 or C1GALT1C1 as a possible way to modulate O-glycan density on EBOV GP for novel vaccine designs and tailored intervention approaches.IMPORTANCEEbola virus glycoprotein acquires its extensive glycan shield in the host cell, where it is decorated with N-linked glycans and mucin-type O-linked glycans. The latter is initiated by a family of polypeptide GalNAc-transferases that have different preferences for optimal peptide substrates resulting in a spectrum of both very selective and redundant substrates for each isoform. In this work, we map the exact locations of O-glycans on Ebola virus glycoprotein and identify subsets of sites preferentially initiated by one of the three key isoforms of GalNAc-Ts, demonstrating that each enzyme contributes to the glycan shield integrity. We further show that altering host O-glycosylation capacity has detrimental effects on Ebola virus replication, with both isoform-specific initiation and elongation playing a role. The combined structural and functional data highlight glycoengineered cell lines as useful tools for investigating molecular mechanisms imposed by specific glycans and for steering the immune responses in future vaccine designs.
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Affiliation(s)
- Ieva Bagdonaite
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Mattia Mirandola
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Denis Pasqual
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Yoshiki Narimatsu
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Hiren J Joshi
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Ali Mirazimi
- Public Health Agency of Sweden, Solna, Sweden
- Department of Laboratory Medicine (LABMED), Karolinska Institute, Stockholm, Sweden
- National Veterinary Institute, Uppsala, Sweden
| | - Hans H Wandall
- Department of Cellular and Molecular Medicine, Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
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41
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Ives CM, Nguyen L, Fogarty CA, Harbison AM, Durocher Y, Klassen J, Fadda E. Role of N343 glycosylation on the SARS-CoV-2 S RBD structure and co-receptor binding across variants of concern. eLife 2024; 13:RP95708. [PMID: 38864493 PMCID: PMC11168744 DOI: 10.7554/elife.95708] [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] [Indexed: 06/13/2024] Open
Abstract
Glycosylation of the SARS-CoV-2 spike (S) protein represents a key target for viral evolution because it affects both viral evasion and fitness. Successful variations in the glycan shield are difficult to achieve though, as protein glycosylation is also critical to folding and structural stability. Within this framework, the identification of glycosylation sites that are structurally dispensable can provide insight into the evolutionary mechanisms of the shield and inform immune surveillance. In this work, we show through over 45 μs of cumulative sampling from conventional and enhanced molecular dynamics (MD) simulations, how the structure of the immunodominant S receptor binding domain (RBD) is regulated by N-glycosylation at N343 and how this glycan's structural role changes from WHu-1, alpha (B.1.1.7), and beta (B.1.351), to the delta (B.1.617.2), and omicron (BA.1 and BA.2.86) variants. More specifically, we find that the amphipathic nature of the N-glycan is instrumental to preserve the structural integrity of the RBD hydrophobic core and that loss of glycosylation at N343 triggers a specific and consistent conformational change. We show how this change allosterically regulates the conformation of the receptor binding motif (RBM) in the WHu-1, alpha, and beta RBDs, but not in the delta and omicron variants, due to mutations that reinforce the RBD architecture. In support of these findings, we show that the binding of the RBD to monosialylated ganglioside co-receptors is highly dependent on N343 glycosylation in the WHu-1, but not in the delta RBD, and that affinity changes significantly across VoCs. Ultimately, the molecular and functional insight we provide in this work reinforces our understanding of the role of glycosylation in protein structure and function and it also allows us to identify the structural constraints within which the glycosylation site at N343 can become a hotspot for mutations in the SARS-CoV-2 S glycan shield.
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Affiliation(s)
- Callum M Ives
- Department of Chemistry, Maynooth UniversityMaynoothIreland
| | - Linh Nguyen
- Department of Chemistry, University of AlbertaEdmontonCanada
| | - Carl A Fogarty
- Department of Chemistry, Maynooth UniversityMaynoothIreland
| | | | - Yves Durocher
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council CanadaQuébecCanada
- Département de Biochimie et Médecine Moléculaire, Université de MontréalQuébecCanada
| | - John Klassen
- Department of Chemistry, University of AlbertaEdmontonCanada
| | - Elisa Fadda
- School of Biological Sciences, University of SouthamptonSouthamptonUnited Kingdom
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Mora-Castaño G, Millán-Jiménez M, Niederquell A, Schönenberger M, Shojaie F, Kuentz M, Caraballo I. Amorphous solid dispersion of a binary formulation with felodipine and HPMC for 3D printed floating tablets. Int J Pharm 2024; 658:124215. [PMID: 38740104 DOI: 10.1016/j.ijpharm.2024.124215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/19/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024]
Abstract
This study focuses on the combination of three-dimensional printing (3DP) and amorphous solid dispersion (ASD) technologies for the manufacturing of gastroretentive floating tablets. Employing hot melt extrusion (HME) and fused deposition modeling (FDM), the study investigates the development of drug-loaded filaments and 3D printed (3DP) tablets containing felodipine as model drug and hydroxypropyl methylcellulose (HPMC) as the polymeric carrier. Prior to fabrication, solubility parameter estimation and molecular dynamics simulations were applied to predict drug-polymer interactions, which are crucial for ASD formation. Physical bulk and surface characterization complemented the quality control of both drug-loaded filaments and 3DP tablets. The analysis confirmed a successful amorphous dispersion of felodipine within the polymeric matrix. Furthermore, the low infill percentage and enclosed design of the 3DP tablet allowed for obtaining low-density systems. This structure resulted in buoyancy during the entire drug release process until a complete dissolution of the 3DP tablets (more than 8 h) was attained. The particular design made it possible for a single polymer to achieve a zero-order controlled release of the drug, which is considered the ideal kinetics for a gastroretentive system. Accordingly, this study can be seen as an advancement in ASD formulation for 3DP technology within pharmaceutics.
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Affiliation(s)
- Gloria Mora-Castaño
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, Universidad de Sevilla, 41012 Seville, Spain
| | - Mónica Millán-Jiménez
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, Universidad de Sevilla, 41012 Seville, Spain.
| | - Andreas Niederquell
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, CH 4132 Muttenz, Switzerland
| | - Monica Schönenberger
- University of Basel, Swiss Nanoscience Institute, Nano Imaging Lab, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Fatemeh Shojaie
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, Universidad de Sevilla, 41012 Seville, Spain
| | - Martin Kuentz
- School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, CH 4132 Muttenz, Switzerland
| | - Isidoro Caraballo
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, Universidad de Sevilla, 41012 Seville, Spain
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Rehman S, Antonovic AK, McIntire IE, Zheng H, Cleaver L, Baczynska M, Adams CO, Portlock T, Richardson K, Shaw R, Oregioni A, Mastroianni G, Whittaker SBM, Kelly G, Lorenz CD, Fornili A, Cianciotto NP, Garnett JA. The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycans. Nat Commun 2024; 15:4912. [PMID: 38851738 PMCID: PMC11162425 DOI: 10.1038/s41467-024-49255-4] [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: 09/16/2023] [Accepted: 05/30/2024] [Indexed: 06/10/2024] Open
Abstract
Bacterial adhesion is a fundamental process which enables colonisation of niche environments and is key for infection. However, in Legionella pneumophila, the causative agent of Legionnaires' disease, these processes are not well understood. The Legionella collagen-like protein (Lcl) is an extracellular peripheral membrane protein that recognises sulphated glycosaminoglycans on the surface of eukaryotic cells, but also stimulates bacterial aggregation in response to divalent cations. Here we report the crystal structure of the Lcl C-terminal domain (Lcl-CTD) and present a model for intact Lcl. Our data reveal that Lcl-CTD forms an unusual trimer arrangement with a positively charged external surface and negatively charged solvent exposed internal cavity. Through molecular dynamics simulations, we show how the glycosaminoglycan chondroitin-4-sulphate associates with the Lcl-CTD surface via distinct binding modes. Our findings show that Lcl homologs are present across both the Pseudomonadota and Fibrobacterota-Chlorobiota-Bacteroidota phyla and suggest that Lcl may represent a versatile carbohydrate-binding mechanism.
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Affiliation(s)
- Saima Rehman
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Anna Katarina Antonovic
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Ian E McIntire
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Huaixin Zheng
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Maria Baczynska
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
- Biological Physics & Soft Matter Research Group, Department of Physics, King's College London, London, UK
| | - Carlton O Adams
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Theo Portlock
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Katherine Richardson
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rosie Shaw
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Alain Oregioni
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Giulia Mastroianni
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, UK
| | - Sara B-M Whittaker
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Christian D Lorenz
- Biological Physics & Soft Matter Research Group, Department of Physics, King's College London, London, UK
| | - Arianna Fornili
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London, UK.
| | - Nicholas P Cianciotto
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
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44
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Cisar JO, Wang X, Woods RJ, Cain KD, Wiens GD. Structural and genetic basis for the binding of a mouse monoclonal antibody to Flavobacterium psychrophilum lipopolysaccharide. JOURNAL OF FISH DISEASES 2024:e13958. [PMID: 38837770 DOI: 10.1111/jfd.13958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/20/2024] [Accepted: 04/08/2024] [Indexed: 06/07/2024]
Abstract
A mouse monoclonal antibody (mAb FL100A) previously prepared against Flavobacterium psychrophilum (Fp) CSF259-93 has now been examined for binding to lipopolysaccharides (LPS) of this strain and Fp 950106-1/1. The corresponding O-polysaccharides (O-PS) of these strains are formed by identical trisaccharide repeats composed of l-Rhamnose (l-Rha), 2-acetamido-2-deoxy-l-fucose (l-FucNAc) and 2-acetamido-4-R1-2,4-dideoxy-d-quinovose (d-Qui2NAc4NR1) where R1 represents a dihydroxyhexanamido moiety. The O-PS loci of these strains are also identical except for the gene (wzy1 or wzy2) that encodes the polysaccharide polymerase. Accordingly, adjacent O-PS repeats are joined through d-Qui2NAc4NR1 and l-Rha by wzy2-dependent α(1-2) linkages in Fp CSF259-93 versus wzy1-dependent β(1-3) linkages in Fp 950106-1/1. mAb FL100A reacted strongly with Fp CSF259-93 O-PS and LPS but weakly or not at all with Fp 950106-1/1 LPS and O-PS. Importantly, it also labelled cell surface blebs on the former but not the latter strain. Additionally, mAb binding was approximately 5-times stronger to homologous Fp CSF259-93 LPS than to LPS from a strain with a different R-group gene. A conformational epitope for mAb FL100A binding was suggested from molecular dynamic simulations of each O-PS. Thus, Fp CSF259-93 O-PS formed a stable well-defined compact helix in which the R1 groups were displayed in a regular pattern on the helix exterior while unreactive Fp 950106-1/1 O-PS adopted a flexible extended linear conformation. Taken together, the findings establish the specificity of mAb FL100A for Wzy2-linked F. psychrophilum O-PS and LPS.
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Affiliation(s)
- John O Cisar
- United States Department of Agricultural Research Service, National Center for Cool and Cold Water Aquaculture, Kearneysville, West Virginia, USA
| | - Xiaocong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Kenneth D Cain
- Department of Fish and Wildlife Resources and the Aquaculture Research Institute, University of Idaho, Moscow, Idaho, USA
- Manchester Research Station, Northwest Fisheries Science Center, NOAA - Fisheries, Port Orchard, Washington, USA
| | - Gregory D Wiens
- United States Department of Agricultural Research Service, National Center for Cool and Cold Water Aquaculture, Kearneysville, West Virginia, USA
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45
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Ali S, Aman A, Hengphasatporn K, Oopkaew L, Todee B, Fujiki R, Harada R, Shigeta Y, Krusong K, Choowongkomon K, Chavasiri W, Wolschann P, Mahalapbutr P, Rungrotmongkol T. Evaluating solubility, stability, and inclusion complexation of oxyresveratrol with various β-cyclodextrin derivatives using advanced computational techniques and experimental validation. Comput Biol Chem 2024; 112:108111. [PMID: 38879954 DOI: 10.1016/j.compbiolchem.2024.108111] [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: 01/24/2024] [Revised: 05/10/2024] [Accepted: 05/23/2024] [Indexed: 06/18/2024]
Abstract
Oxyresveratrol (OXY), a natural stilbenoid in mulberry fruits, is known for its diverse pharmacological properties. However, its clinical use is hindered by low water solubility and limited bioavailability. In the present study, the inclusion complexes of OXY with β-cyclodextrin (βCD) and its three analogs, dimethyl-β-cyclodextrin (DMβCD), hydroxypropyl-β-cyclodextrin (HPβCD) and sulfobutylether-β-cyclodextrin (SBEβCD), were investigated using in silico and in vitro studies. Molecular docking revealed two binding orientations of OXY, namely, 4',6'-dihydroxyphenyl (A-form) and 5,7-benzenediol ring (B-form). Molecular Dynamics simulations suggested the formation of inclusion complexes with βCDs through two distinct orientations, with OXY/SBEβCD exhibiting maximum atom contacts and the lowest solvent-exposed area in the hydrophobic cavity. These results corresponded well with the highest binding affinity observed in OXY/SBEβCD when assessed using the MM/GBSA method. Beyond traditional simulation methods, Ligand-binding Parallel Cascade Selection Molecular Dynamics method was employed to investigate how the drug enters and accommodates within the hydrophobic cavity. The in silico results aligned with stability constants: SBEβCD (2060 M-1), HPβCD (1860 M-1), DMβCD (1700 M-1), and βCD (1420 M-1). All complexes exhibited a 1:1 binding mode (AL type), with SBEβCD enhancing OXY solubility (25-fold). SEM micrographs, DSC thermograms, FT-IR and 1H NMR spectra confirm the inclusion complex formation, revealing novel surface morphologies, distinctive thermal behaviors, and new peaks. Notably, the inhibitory impact on the proliferation of breast cancer cell lines, MCF-7, exhibited by inclusion complexes particularly OXY/DMβCD, OXY/HPβCD, and OXY/SBEβCD were markedly superior compared to that of OXY alone.
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Affiliation(s)
- Saba Ali
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Aamir Aman
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kowit Hengphasatporn
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Lipika Oopkaew
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Bunyaporn Todee
- Department of Chemistry, Faculty of Science, Mahidol University, Rama VI Rd, Bangkok 10400, Thailand
| | - Ryo Fujiki
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan
| | - Kuakarun Krusong
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Warinthorn Chavasiri
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Peter Wolschann
- Institute of Theoretical Chemistry, University of Vienna, Vienna 1090, Austria
| | - Panupong Mahalapbutr
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.
| | - Thanyada Rungrotmongkol
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.
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46
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Sun Z, Zhang Z, Wang X, An H, Liang S, Li N. Preparation and characterization of cellulose fluorescent material: Experiment and simulation. Int J Biol Macromol 2024; 270:132064. [PMID: 38719012 DOI: 10.1016/j.ijbiomac.2024.132064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 05/20/2024]
Abstract
The extensive use of fossil based materials has caused serious pollution problems, the full utilization of biomass resources to prepare high value-added new materials is of great significance for the environmental protection and sustainable social development. For this purpose, this study explored the preparation process and molecular dynamics simulation of cellulose fluorescent materials. Firstly, bacterial cellulose was dissolved in a solution of NaOH and urea at low temperature, followed by a solution blending and hot pressing with hyperbranched polyamide. It was found that the addition of hyperbranched polyamide could effectively filled in the internal pores of cellulose hydrogel, thereby enhancing the fluorescence effects and tensile properties, especially the elongation at break of cellulose materials. The optimal amount of hyperbranched polyamide added was 5 wt%. Molecular dynamics simulation showed that the hydrogen bonds and interaction with cellulose increased as the concentration of hyperbranched polyamide increased.
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Affiliation(s)
- Zhanying Sun
- School of Materials Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China; Hebei Key Laboratory of Flexible Functional Materials, Hebei University of Science and Technology, Shijiazhuang 050018, China.
| | - Zhichao Zhang
- School of Materials Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Xin Wang
- School of Materials Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China; Hebei Key Laboratory of Flexible Functional Materials, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Haoran An
- School of Materials Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China; Hebei Key Laboratory of Flexible Functional Materials, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Shuang Liang
- School of Materials Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China; Hebei Key Laboratory of Flexible Functional Materials, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Na Li
- School of Materials Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China; Hebei Key Laboratory of Flexible Functional Materials, Hebei University of Science and Technology, Shijiazhuang 050018, China
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47
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Adolf-Bryfogle J, Labonte JW, Kraft JC, Shapovalov M, Raemisch S, Lütteke T, DiMaio F, Bahl CD, Pallesen J, King NP, Gray JJ, Kulp DW, Schief WR. Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design. PLoS Comput Biol 2024; 20:e1011895. [PMID: 38913746 PMCID: PMC11288642 DOI: 10.1371/journal.pcbi.1011895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/30/2024] [Accepted: 02/06/2024] [Indexed: 06/26/2024] Open
Abstract
Carbohydrates and glycoproteins modulate key biological functions. However, experimental structure determination of sugar polymers is notoriously difficult. Computational approaches can aid in carbohydrate structure prediction, structure determination, and design. In this work, we developed a glycan-modeling algorithm, GlycanTreeModeler, that computationally builds glycans layer-by-layer, using adaptive kernel density estimates (KDE) of common glycan conformations derived from data in the Protein Data Bank (PDB) and from quantum mechanics (QM) calculations. GlycanTreeModeler was benchmarked on a test set of glycan structures of varying lengths, or "trees". Structures predicted by GlycanTreeModeler agreed with native structures at high accuracy for both de novo modeling and experimental density-guided building. We employed these tools to design de novo glycan trees into a protein nanoparticle vaccine to shield regions of the scaffold from antibody recognition, and experimentally verified shielding. This work will inform glycoprotein model prediction, glycan masking, and further aid computational methods in experimental structure determination and refinement.
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Affiliation(s)
- Jared Adolf-Bryfogle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, United States of America
- Institute for Protein Innovation, Boston, Massachusetts, United States of America
- Division of Hematology-Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jason W. Labonte
- Department of Chemistry & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - John C. Kraft
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Maxim Shapovalov
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Sebastian Raemisch
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, United States of America
| | - Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Giessen, Germany
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Christopher D. Bahl
- Institute for Protein Innovation, Boston, Massachusetts, United States of America
- Division of Hematology-Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jesper Pallesen
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Jeffrey J. Gray
- Department of Chemistry & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Daniel W. Kulp
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - William R. Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, California, United States of America
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48
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Higuchi Y, Saleh MA, Anada T, Tanaka M, Hishida M. Rotational Dynamics of Water near Osmolytes by Molecular Dynamics Simulations. J Phys Chem B 2024; 128:5008-5017. [PMID: 38728154 DOI: 10.1021/acs.jpcb.3c08470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
The behavior of water molecules around organic molecules has attracted considerable attention as a crucial factor influencing the properties and functions of soft matter and biomolecules. Recently, it has been suggested that the change in protein stability upon the addition of small organic molecules (osmolytes) is dominated by the change in the water dynamics caused by the osmolyte, where the dynamics of not only the directly interacting water molecules but also the long-range hydration layer affect the protein stability. However, the relation between the long-range structure of hydration water in various solutions and the water dynamics remains unclear at the molecular level. We performed density-functional tight-binding molecular dynamics simulations to elucidate the varying rotational dynamics of water molecules in 15 osmolyte solutions. A positive correlation was observed between the rotational relaxation time and our proposed normalized parameter obtained by dividing the number of hydrogen bonds between water molecules by the number of nearest-neighbor water molecules. For the 15 osmolyte solutions, an increase or a decrease in the value of the normalized parameter for the second hydration shell tended to result in water molecules with slow and fast rotational dynamics, respectively, thus illustrating the importance of the second hydration shell for the rotational dynamics of water molecules. Our simulation results are anticipated to advance the current understanding of water dynamics around organic molecules and the long-range structure of water molecules.
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Affiliation(s)
- Yuji Higuchi
- Research Institute for Information Technology, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Md Abu Saleh
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Takahisa Anada
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Masaru Tanaka
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Mafumi Hishida
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo 162-8601, Japan
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49
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Ma B, Chen H, Gong J, Liu W, Wei X, Zhang Y, Li X, Li M, Wang Y, Shang S, Tian B, Li Y, Wang R, Tan Z. Enhancing Protein Solubility via Glycosylation: From Chemical Synthesis to Machine Learning Predictions. Biomacromolecules 2024; 25:3001-3010. [PMID: 38598264 DOI: 10.1021/acs.biomac.4c00134] [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: 04/11/2024]
Abstract
Glycosylation is a valuable tool for modulating protein solubility; however, the lack of reliable research strategies has impeded efficient progress in understanding and applying this modification. This study aimed to bridge this gap by investigating the solubility of a model glycoprotein molecule, the carbohydrate-binding module (CBM), through a two-stage process. In the first stage, an approach involving chemical synthesis, comparative analysis, and molecular dynamics simulations of a library of glycoforms was employed to elucidate the effect of different glycosylation patterns on solubility and the key factors responsible for the effect. In the second stage, a predictive mathematical formula, innovatively harnessing machine learning algorithms, was derived to relate solubility to the identified key factors and accurately predict the solubility of the newly designed glycoforms. Demonstrating feasibility and effectiveness, this two-stage approach offers a valuable strategy for advancing glycosylation research, especially for the discovery of glycoforms with increased solubility.
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Affiliation(s)
- Bo Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Hedi Chen
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Jinyuan Gong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wenqiang Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xiuli Wei
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yajing Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xin Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Meng Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yani Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shiying Shang
- Center of Pharmaceutical Technology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Boxue Tian
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yaohao Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ruihan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Chemical Engineering College, Hebei Normal University of Science and Technology, Qinhuangdao 066600, China
| | - Zhongping Tan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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Maity S, Pahari S, Santra S, Jana M. Interfacial Glucose to Regulate Hydrated Lipid Bilayer Properties: Influence of Concentrations. J Chem Inf Model 2024; 64:3841-3854. [PMID: 38635679 DOI: 10.1021/acs.jcim.3c01991] [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: 04/20/2024]
Abstract
A series of atomistic molecular dynamics (MD) simulations were carried out with a hydrated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer with the variation of glucose concentrations from 0 to 30 wt % in the presence of 0.3 M NaCl. The study suggested that although the thickness of the lipid bilayer dropped significantly with the increase in glucose concentration, it expanded laterally at high glucose levels due to the intercalation of glucose between the headgroups of adjacent lipids. We adopted the surface assessment via the grid evaluation method to compute the deviation of the bilayer's key structural features for the different amounts of glucose present. This suggested that the accumulation of glucose molecules near the headgroups influences the local lipid bilayer undulation and crimping of the lipid tails. We find that the area compressibility modulus increases with the glucose level, causing enhanced bilayer rigidity arising from the slow lateral diffusion of lipids. The restricted lipid motion at high glucose concentrations controls the sustainability of the curved bilayer surface. Calculations revealed that certain orientations of CO → of interfacial glucose with the PN → of lipid headgroups are preferred, which helps the glucose to form direct hydrogen bonds (HBs) with the lipid headgroups. Such lipid-glucose (LG) HBs relax slowly at low glucose concentrations and exhibit a higher lifetime, whereas fast structural relaxation of LG HBs with a shorter lifetime was noticed at a higher glucose level. In contrast, lipid-water (LW) HBs exhibited a higher lifetime at a higher glucose level, which gradually decreased with the glucose level lowering. The study interprets that the glucose concentration-driven LW and LG interactions are mutually inclusive. Our detailed analysis will exemplify small saccharide concentration-driven membrane stabilizing efficiency, which is, in general, helpful for drug delivery study.
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Affiliation(s)
- Sankar Maity
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Somdev Pahari
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Santanu Santra
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
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