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Bolshchikov BD, Tsvetkov VB, Alikhanova OL, Serbin AV. How to Fight Kinetics in Complex Radical Polymerization Processes: Theoretical Case Study of Poly(divinyl ether‐alt‐maleic anhydride). MACROMOL CHEM PHYS 2019. [DOI: 10.1002/macp.201900389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Boris D. Bolshchikov
- Polyelectrolytes and Biomedical Polymers Laboratory A.V. Topchiev Institute of Petrochemical Synthesis RAS, Leninsky prospect, 29 Moscow 119991 Russia
| | - Vladimir B. Tsvetkov
- Polyelectrolytes and Biomedical Polymers Laboratory A.V. Topchiev Institute of Petrochemical Synthesis RAS, Leninsky prospect, 29 Moscow 119991 Russia
- Department of Molecular VirologyFSBI Research Institute of Influenza Ministry of Health of the Russian Federation Professor Popov Street 15/17 Saint Petersburg 197376 Russia
- Federal Research and Clinical Centre of Physical‐Chemical Medicine Federal Medical Biological Agency Malaya Pirogovskaya 1a Moscow 119435 Russia
- Computational Oncology Group I.M. Sechenov First Moscow State Medical University Trubetskaya Str. 8‐2 119991 Moscow Russia
| | - Olga L. Alikhanova
- Polyelectrolytes and Biomedical Polymers Laboratory A.V. Topchiev Institute of Petrochemical Synthesis RAS, Leninsky prospect, 29 Moscow 119991 Russia
- Research Center for Biomodulators and Drugs Health Research and Development Foundation Admiral Ushakov Boulevard 14–209 Moscow 117042 Russia
| | - Alexander V. Serbin
- Polyelectrolytes and Biomedical Polymers Laboratory A.V. Topchiev Institute of Petrochemical Synthesis RAS, Leninsky prospect, 29 Moscow 119991 Russia
- Research Center for Biomodulators and Drugs Health Research and Development Foundation Admiral Ushakov Boulevard 14–209 Moscow 117042 Russia
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Shin J, Li S. Utilization of a Multiple Cloning Site as a Versatile Platform for DNA Triblock Copolymer Synthesis. Bioconjug Chem 2019; 30:2563-2572. [PMID: 31545903 DOI: 10.1021/acs.bioconjchem.9b00503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA-containing block copolymers have utility in a wide range of biomedical applications. However, synthesis of these hybrid materials, especially ones with complex chain structures, remains to be a major challenge. Here, we report the use of a combination of restriction enzyme sites and ligation enzymes to synthesize DNA triblock copolymers. In contrast to triblock structures held together by DNA hybridization, the newly synthesized DNA triblocks have all blocks connected by covalent bonds. The improved stability of the triblocks against environmental factors such as urea denaturing is confirmed. Furthermore, we incorporate a multiple cloning site (MCS) into the DNA block copolymers and show that the restriction sites can be cut by their corresponding restriction enzymes, generating diblocks with different sticky ends. By utilizing these sticky ends of specific sequences, the cut diblocks are further ligated to create a variety of triblock copolymers with different DNA center blocks and synthetic polymer end blocks. This study presents a versatile platform based on MCS for the synthesis and regeneration of a range of DNA-containing block copolymers.
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Affiliation(s)
- Jeehae Shin
- Department of Chemical and Biomolecular Engineering , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , South Korea
| | - Sheng Li
- Department of Chemical and Biomolecular Engineering , Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 , South Korea
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Bolshchikov BD, Tsvetkov VB, Alikhanova OL, Serbin AV. [Modeling and theoretical analysis of ring specific mimicry in view of isomerism within medicinal promising oligomers of "DIVEMA"]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2019; 65:133-151. [PMID: 30950818 DOI: 10.18097/pbmc20196502133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The furan or pyran related hetero cycles play basic role in structural units of nucleic acids (NA) and polysaccharides (PS), significantly predetermining their functional specifics. Some of such properties, in great relevancy for medicine, can be imitated through mimicry of polymers synthetic. Particularly, a formation of similar cycloisomeric chains is possible in process of free-radical cyclocopolymerization of divinyl ether (DVE) and maleic anhydride (MA). The products yielded (DVEMA) of general formula [DVE(MA)-alt-MA]n become precursors for a broad family of water-soluble derivatives capable of wide spectrum of bioactivity, including induction of interferon, immune-stimulated and direct antiviral protection. In this connection, the knowledge: what is content of different heterocyclic isomers in backbone of the preparations and what their partial contributions in promotion of the certain bioactivities observed, are in great importance. Available experimental data (NMR, IR, etc.), controversial for interpretations, didn't elucidate a required estimation of the DVEMA isomerism. The current work represents an independent exploration of the problem via quantum chemistry-based analysis of kinetic (activation barriers) and thermodynamic (enthalpies) priorities in competition between variable isomerism within the chain synthesis. The system is considered in maximal range of hypothetically allowable variations of two levels for double regioselective bifurcations: there are four competitive ways, each of which involves a sequence of four type elementary reactions for a diverse-isomeric formation of chain units. A genesis of six chiral centers (62 stereoisomers permitted) per every of the four part ways was accounted in view for up to 256 isomeric variations in total. The required time-minimized but precisely accurate computations were conducted via B3LYP/6-31G(d), M06-2X/6-311+G(d), M06-2X/6-31+G(2df,p) techniques, which were preselected through model test-systems. As a result, the mechanisms, crucial points and factors for the process-permitted regulation of isomeric content of DVEMA were studied in details. The narrow enough set of most probable enantiomers within highly competitive 5-exo- and 6-endo- ring closing sub-ways was revealed. The results obtained are very actual for an adequate modeling (docking / molecular dynamics) of DVEMA derivatives in their interactions with biopolymer targets, in search for purposed advancement of current background in design and synthesis of highly effective agents for combined antiviral protection (against HIV, flu, herpes, and other infections).
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Affiliation(s)
- B D Bolshchikov
- Topchiev Institute of Petrochemical Synthesis, RAS, Moscow, Russia
| | - V B Tsvetkov
- Research Center for Biomodulators, Health Research and Development Foundation, Moscow, Russia
| | - O L Alikhanova
- Topchiev Institute of Petrochemical Synthesis, RAS, Moscow, Russia; Research Center for Biomodulators, Health Research and Development Foundation, Moscow, Russia
| | - A V Serbin
- Topchiev Institute of Petrochemical Synthesis, RAS, Moscow, Russia; Research Center for Biomodulators, Health Research and Development Foundation, Moscow, Russia
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Mosquera-Giraldo LI, Borca CH, Parker AS, Dong Y, Edgar KJ, Beaudoin SP, Slipchenko LV, Taylor LS. Crystallization Inhibition Properties of Cellulose Esters and Ethers for a Group of Chemically Diverse Drugs: Experimental and Computational Insight. Biomacromolecules 2018; 19:4593-4606. [PMID: 30376299 DOI: 10.1021/acs.biomac.8b01280] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Laura I. Mosquera-Giraldo
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana, United States
| | - Carlos H. Borca
- Department of Chemistry, College of Science, Purdue University, West Lafayette, Indiana, United States
| | - Andrew S. Parker
- Department of Chemical Engineering, College of Engineering, Purdue University, West Lafayette, Indiana, United States
| | - Yifan Dong
- Department of Chemistry, College of Science, Virginia Tech, Blacksburg, Virginia, United States
| | - Kevin J. Edgar
- Department of Sustainable Biomaterials, College of Natural Resources and Environment, Virginia Tech, Blacksburg, Virginia, United States
| | - Stephen P. Beaudoin
- Department of Chemical Engineering, College of Engineering, Purdue University, West Lafayette, Indiana, United States
| | - Lyudmila V. Slipchenko
- Department of Chemistry, College of Science, Purdue University, West Lafayette, Indiana, United States
| | - Lynne S. Taylor
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana, United States
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Zabrodskaya YA, Shvetsov AV, Tsvetkov VB, Egorov VV. A double-edged sword: supramolecular complexes of triazavirine display multicenter binding effects which influence aggregate formation. J Biomol Struct Dyn 2018; 37:3041-3047. [PMID: 30073907 DOI: 10.1080/07391102.2018.1507837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yana A Zabrodskaya
- a Molecular Biology of Viruses Department, Smorodintsev Research Institute of Influenza , Ministry of Healthcare of the Russian Federation , St. Petersburg , Russia.,b Molecular and Radiation Biophysics Department , Petersburg Nuclear Physics Institute named by B. P. Konstantinov of National Research Center "Kurchatov Institute" , Gatchina , Russia
| | - Alexey V Shvetsov
- b Molecular and Radiation Biophysics Department , Petersburg Nuclear Physics Institute named by B. P. Konstantinov of National Research Center "Kurchatov Institute" , Gatchina , Russia.,c Supercomputer Center , Peter the Great Saint-Petersburg State Polytechnic University , St. Petersburg , Russia
| | - Vladimir B Tsvetkov
- a Molecular Biology of Viruses Department, Smorodintsev Research Institute of Influenza , Ministry of Healthcare of the Russian Federation , St. Petersburg , Russia.,d Biophysics Department , Research and Clinical Center for Physical Chemical Medicine , Moscow , Russia.,e Polyelectrolytes and Biomedical Polymers Laboratory , A.V. Topchiev Institute of Petrochemical Synthesis , RAS Moscow , Russia
| | - Vladimir V Egorov
- a Molecular Biology of Viruses Department, Smorodintsev Research Institute of Influenza , Ministry of Healthcare of the Russian Federation , St. Petersburg , Russia.,b Molecular and Radiation Biophysics Department , Petersburg Nuclear Physics Institute named by B. P. Konstantinov of National Research Center "Kurchatov Institute" , Gatchina , Russia.,f Molecular Genetics Department , Federal State Budgetary Scientific Institution "Institute of Experimental Medicine" , St. Petersburg , Russia
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Bolshchikov BD, Tsvetkov VB, Serbin AV. Practical procedure for a theoretical investigation of thermodynamics and kinetics aspects of different-scale radical reactions from addition and cyclization to cyclocopolymerization involving maleic anhydride and divinyl ether. POLYMER 2018. [DOI: 10.1016/j.polymer.2018.05.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Savage AM, Li Y, Matolyak LE, Doncel GF, Turner SR, Gandour RD. Anti-HIV Activities of Precisely Defined, Semirigid, Carboxylated Alternating Copolymers. J Med Chem 2014; 57:6354-63. [DOI: 10.1021/jm401913w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Alice M. Savage
- Department
of Chemistry MC0212 and Macromolecules and Interfaces Institute MC0344, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Yi Li
- Department
of Chemistry MC0212 and Macromolecules and Interfaces Institute MC0344, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Lindsay E. Matolyak
- Department
of Chemistry MC0212 and Macromolecules and Interfaces Institute MC0344, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Gustavo F. Doncel
- CONRAD, Eastern Virginia Medical School, 601 Colley Avenue, Norfolk, Virginia 23507, United States
| | - S. Richard Turner
- Department
of Chemistry MC0212 and Macromolecules and Interfaces Institute MC0344, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Richard D. Gandour
- Department
of Chemistry MC0212 and Macromolecules and Interfaces Institute MC0344, Virginia Tech, Blacksburg, Virginia 24061, United States
- Virginia
Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
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Tsvetkov VB, Serbin AV. Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking: anchors modified polyanions interference with the HIV-1 fusion mediator. J Comput Aided Mol Des 2014; 28:647-73. [PMID: 24862639 PMCID: PMC4050303 DOI: 10.1007/s10822-014-9749-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 05/05/2014] [Indexed: 11/28/2022]
Abstract
In previous works we reported the design, synthesis and in vitro evaluations of synthetic anionic polymers modified by alicyclic pendant groups (hydrophobic anchors), as a novel class of inhibitors of the human immunodeficiency virus type 1 (HIV-1) entry into human cells. Recently, these synthetic polymers interactions with key mediator of HIV-1 entry-fusion, the tri-helix core of the first heptad repeat regions [HR1]3 of viral envelope protein gp41, were pre-studied via docking in terms of newly formulated algorithm for stepwise approximation from fragments of polymeric backbone and side-group models toward real polymeric chains. In the present article the docking results were verified under molecular dynamics (MD) modeling. In contrast with limited capabilities of the docking, the MD allowed of using much more large models of the polymeric ligands, considering flexibility of both ligand and target simultaneously. Among the synthesized polymers the dinorbornen anchors containing alternating copolymers of maleic acid were selected as the most representative ligands (possessing the top anti-HIV activity in vitro in correlation with the highest binding energy in the docking). To verify the probability of binding of the polymers with the [HR1]3 in the sites defined via docking, various starting positions of polymer chains were tried. The MD simulations confirmed the main docking-predicted priority for binding sites, and possibilities for axial and belting modes of the ligands-target interactions. Some newly MD-discovered aspects of the ligand's backbone and anchor units dynamic cooperation in binding the viral target clarify mechanisms of the synthetic polymers anti-HIV activity and drug resistance prevention.
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Affiliation(s)
- Vladimir B. Tsvetkov
- Biomodulators and Drugs Research Center, Health RDF, Adm. Ushakova 14-209, 117042 Moscow, Russia
- Topchiev Institute of Petrochemical Synthesis, RAS, Leninsky Pr. 29, 119991 Moscow, Russia
- Institute for Physical-Chemical Medicine, Malaya Pirogovskaya Str. 1a, 119828 Moscow, Russia
| | - Alexander V. Serbin
- Biomodulators and Drugs Research Center, Health RDF, Adm. Ushakova 14-209, 117042 Moscow, Russia
- Topchiev Institute of Petrochemical Synthesis, RAS, Leninsky Pr. 29, 119991 Moscow, Russia
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