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Danielsson A, Samsonov SA, Liwo A, Sieradzan AK. Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin. J Chem Theory Comput 2023; 19:6023-6036. [PMID: 37587433 PMCID: PMC10500997 DOI: 10.1021/acs.jctc.3c00511] [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: 05/17/2023] [Indexed: 08/18/2023]
Abstract
Heparin is an unbranched periodic polysaccharide composed of negatively charged monomers and involved in key biological processes, including anticoagulation, angiogenesis, and inflammation. Its structure and dynamics have been studied extensively using experimental as well as theoretical approaches. The conventional approach of computational chemistry applied to the analysis of biomolecules is all-atom molecular dynamics, which captures the interactions of individual atoms by solving Newton's equation of motion. An alternative is molecular dynamics simulations using coarse-grained models of biomacromolecules, which offer a reduction of the representation and consequently enable us to extend the time and size scale of simulations by orders of magnitude. In this work, we extend the UNIfied COarse-gRaiNed (UNICORN) model of biological macromolecules developed in our laboratory to heparin. We carried out extensive tests to estimate the optimal weights of energy terms of the effective energy function as well as the optimal Debye-Hückel screening factor for electrostatic interactions. We applied the model to study unbound heparin molecules of polymerization degree ranging from 6 to 68 residues. We compare the obtained coarse-grained heparin conformations with models obtained from X-ray diffraction studies of heparin. The SUGRES-1P force field was able to accurately predict the general shape and global characteristics of heparin molecules.
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Affiliation(s)
- Annemarie Danielsson
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Sergey A. Samsonov
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam Liwo
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam K. Sieradzan
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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Thalhammer A, Bröker NK. Biophysical Approaches for the Characterization of Protein-Metabolite Interactions. Methods Mol Biol 2023; 2554:199-229. [PMID: 36178628 DOI: 10.1007/978-1-0716-2624-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
With an estimate of hundred thousands of protein molecules per cell and the number of metabolites several orders of magnitude higher, protein-metabolite interactions are omnipresent. In vitro analyses are one of the main pillars on the way to establish a solid understanding of how these interactions contribute to maintaining cellular homeostasis. A repertoire of biophysical techniques is available by which protein-metabolite interactions can be quantitatively characterized in terms of affinity, specificity, and kinetics in a broad variety of solution environments. Several of those provide information on local or global conformational changes of the protein partner in response to ligand binding. This review chapter gives an overview of the state-of-the-art biophysical toolbox for the study of protein-metabolite interactions. It briefly introduces basic principles, highlights recent examples from the literature, and pinpoints promising future directions.
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Affiliation(s)
- Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Potsdam, Germany.
| | - Nina K Bröker
- Physical Biochemistry, University of Potsdam, Potsdam, Germany
- Health and Medical University Potsdam, Potsdam, Germany
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Royo-Rubio E, Martín-Cañadilla V, Rusnati M, Milanesi M, Lozano-Cruz T, Gómez R, Jiménez JL, Muñoz-Fernández MÁ. Prevention of Herpesviridae Infections by Cationic PEGylated Carbosilane Dendrimers. Pharmaceutics 2022; 14:pharmaceutics14030536. [PMID: 35335912 PMCID: PMC8950866 DOI: 10.3390/pharmaceutics14030536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 12/28/2022] Open
Abstract
Infections caused by viruses from the Herpesviridae family produce some of the most prevalent transmitted diseases in the world, constituting a serious global public health issue. Some of the virus properties such as latency and the appearance of resistance to antiviral treatments complicate the development of effective therapies capable of facing the infection. In this context, dendrimers present themselves as promising alternatives to current treatments. In this study, we propose the use of PEGylated cationic carbosilane dendrimers as inhibitors of herpes simplex virus 2 (HSV-2) and human cytomegalovirus (HCMV)infections. Studies of mitochondrial toxicity, membrane integrity, internalization and viral infection inhibition indicated that G2-SN15-PEG, G3-SN31-PEG, G2-SN15-PEG fluorescein isothiocyanate (FITC) labeled and G3-SN31-PEG-FITC dendrimers are valid candidates to target HSV-2 and HCMV infections since they are biocompatible, can be effectively internalized and are able to significantly inhibit both infections. Later studies (including viral inactivation, binding inhibition, heparan sulphate proteoglycans (HSPG)binding and surface plasmon resonance assays) confirmed that inhibition takes place at first infection stages. More precisely, these studies established that their attachment to cell membrane heparan sulphate proteoglycans impede the interaction between viral glycoproteins and these cell receptors, thus preventing infection. Altogether, our research confirmed the high capacity of these PEGylated carbosilane dendrimers to prevent HSV-2 and HCMV infections, making them valid candidates as antiviral agents against Herpesviridae infections.
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Affiliation(s)
- Elena Royo-Rubio
- Laboratorio InmunoBiologia Molecular, Instituto Investigacion Sanitaria Gregorio Maranon (IiSGM), Hospital General Universitario Gregorio Maranon (HGUGM), 28009 Madrid, Spain; (E.R.-R.); (V.M.-C.)
- Plataforma de Laboratorio (Inmunologia), HGUGM, IiSGM, Spanish HIV HGM BioBank, 28009 Madrid, Spain;
| | - Vanessa Martín-Cañadilla
- Laboratorio InmunoBiologia Molecular, Instituto Investigacion Sanitaria Gregorio Maranon (IiSGM), Hospital General Universitario Gregorio Maranon (HGUGM), 28009 Madrid, Spain; (E.R.-R.); (V.M.-C.)
- Plataforma de Laboratorio (Inmunologia), HGUGM, IiSGM, Spanish HIV HGM BioBank, 28009 Madrid, Spain;
| | - Marco Rusnati
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (M.R.); (M.M.)
| | - Maria Milanesi
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (M.R.); (M.M.)
| | - Tania Lozano-Cruz
- Departmento Quimica Organica y Quimica Inorganica, Instituto de Investigacion Quimica “Andres M. del Rio″ (IQAR), Universidad de Alcalá (IRYCIS), Campus Universitario, 28871 Madrid, Spain; (T.L.-C.); (R.G.)
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - Rafael Gómez
- Departmento Quimica Organica y Quimica Inorganica, Instituto de Investigacion Quimica “Andres M. del Rio″ (IQAR), Universidad de Alcalá (IRYCIS), Campus Universitario, 28871 Madrid, Spain; (T.L.-C.); (R.G.)
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - José Luís Jiménez
- Plataforma de Laboratorio (Inmunologia), HGUGM, IiSGM, Spanish HIV HGM BioBank, 28009 Madrid, Spain;
| | - Maria Ángeles Muñoz-Fernández
- Laboratorio InmunoBiologia Molecular, Instituto Investigacion Sanitaria Gregorio Maranon (IiSGM), Hospital General Universitario Gregorio Maranon (HGUGM), 28009 Madrid, Spain; (E.R.-R.); (V.M.-C.)
- Correspondence: or
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Xie J, Shen Q, Huang K, Zheng T, Cheng L, Zhang Z, Yu Y, Liao G, Wang X, Li C. Oriented Assembly of Cell-Mimicking Nanoparticles via a Molecular Affinity Strategy for Targeted Drug Delivery. ACS NANO 2019; 13:5268-5277. [PMID: 31022341 DOI: 10.1021/acsnano.8b09681] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Cell membrane cloaking is an emerging field in drug delivery in which specific functions of parent cells are conferred to newly formed biomimetic vehicles. A growing variety of delivery systems with diverse surface properties have been utilized for this strategy, but it is unclear whether the affinity of membrane-core pairs could guarantee effective and proper camouflaging. In this study, we propose a concise and effective "molecular affinity" strategy using the intracellular domain of transmembrane receptors as "grippers" during membrane coating. Red blood cell (RBC) membranes and cationic liposomes were adopted for fabrication, and a peptide ligand derived from the cytoplasmic protein P4.2 was prepared to specifically recognize the cytoplasmic domain of band 3, a key transmembrane receptor of erythrocytes. Once anchored onto the liposome surface, the P4.2-derived peptide would interact with the isolated RBC membrane, forming a "hidden peptide button", which ensures the right-side-out orientation. The membrane-coated liposomes exhibited an appropriate size distribution around 100 nm and high stability, with superior circulation durations compared with those of conventional PEGylated liposomes. Importantly, they possessed the ability to target Candida albicans by the interaction between the pathogenic fungus and host erythrocytes and to neutralize hemotoxin secreted by the pathogenic fungi. The curative effect of the model drug was thus substantially improved. In summary, the "molecular affinity" strategy may provide a powerful and universal approach for the construction of cell membrane-coated biomaterials and nanomedicines at both laboratory and industrial scales.
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Affiliation(s)
- Jing Xie
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , China
| | - Qing Shen
- Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai , 200032 China
| | - Kexin Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , China
| | - Tingyu Zheng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , China
| | - Liting Cheng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , China
| | - Zhen Zhang
- Department of Clinical Laboratory , Chongqing General Hospital , Chongqing , 400014 , China
| | - Yang Yu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , China
| | - Guojian Liao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , China
| | - Xiaoyou Wang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , China
| | - Chong Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences , Southwest University , Chongqing , 400715 , China
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