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Kostromina MA, Tukhovskaya EA, Shaykhutdinova ER, Palikova YA, Palikov VA, Slashcheva GA, Ismailova AM, Kravchenko IN, Dyachenko IA, Zayats EA, Abramchik YA, Murashev AN, Esipov RS. Unified Methodology for the Primary Preclinical In Vivo Screening of New Anticoagulant Pharmaceutical Agents from Hematophagous Organisms. Int J Mol Sci 2024; 25:3986. [PMID: 38612796 PMCID: PMC11011928 DOI: 10.3390/ijms25073986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/29/2024] [Accepted: 03/30/2024] [Indexed: 04/14/2024] Open
Abstract
The development of novel anticoagulants requires a comprehensive investigational approach that is capable of characterizing different aspects of antithrombotic activity. The necessary experiments include both in vitro assays and studies on animal models. The required in vivo approaches include the assessment of pharmacokinetic and pharmacodynamic profiles and studies of hemorrhagic and antithrombotic effects. Comparison of anticoagulants with different mechanisms of action and administration types requires unification of the experiment scheme and its adaptation to existing laboratory conditions. The rodent thrombosis models in combination with the assessment of hemostasis parameters and hematological analysis are the classic methods for conducting preclinical studies. We report an approach for the comparative study of the activity of different anticoagulants in vivo, including the investigation of pharmacodynamics and the assessment of hemorrhagic effects (tail-cut bleeding model) and pathological thrombus formation (inferior vena cava stenosis model of venous thrombosis). The reproducibility and uniformity of our set of experiments were illustrated on unfractionated heparin and dabigatran etexilate (the most common pharmaceuticals in antithrombic therapy) as comparator drugs and an experimental drug variegin from the tick Amblyomma variegatum. Variegin is notorious since it is a potential analogue of bivalirudin (Angiomax, Novartis AG, Basel, Switzerland), which is now being actively introduced into antithrombotic therapy.
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Affiliation(s)
- Maria A. Kostromina
- Laboratory of Biopharmaceutical Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia
| | - Elena A. Tukhovskaya
- Biological Testing Laboratory, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, ProspektNauki, 6, 142290 Moscow, Russia
| | - Elvira R. Shaykhutdinova
- Biological Testing Laboratory, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, ProspektNauki, 6, 142290 Moscow, Russia
| | - Yuliya A. Palikova
- Biological Testing Laboratory, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, ProspektNauki, 6, 142290 Moscow, Russia
| | - Viktor A. Palikov
- Biological Testing Laboratory, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, ProspektNauki, 6, 142290 Moscow, Russia
| | - Gulsara A. Slashcheva
- Biological Testing Laboratory, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, ProspektNauki, 6, 142290 Moscow, Russia
| | - Alina M. Ismailova
- Biological Testing Laboratory, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, ProspektNauki, 6, 142290 Moscow, Russia
| | - Irina N. Kravchenko
- Biological Testing Laboratory, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, ProspektNauki, 6, 142290 Moscow, Russia
| | - Igor A. Dyachenko
- Biological Testing Laboratory, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, ProspektNauki, 6, 142290 Moscow, Russia
| | - Evgeniy A. Zayats
- Laboratory of Biopharmaceutical Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia
| | - Yuliya A. Abramchik
- Laboratory of Biopharmaceutical Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia
| | - Arkady N. Murashev
- Biological Testing Laboratory, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, ProspektNauki, 6, 142290 Moscow, Russia
| | - Roman S. Esipov
- Laboratory of Biopharmaceutical Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia
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Lykoshin DD, Kostromina MA, Azmukova VR, Esipov RS. Chaperone-mediated production of active homodimer human bone morphogenetic protein - 2 in E. coli. Protein Expr Purif 2023; 206:106245. [PMID: 36805029 DOI: 10.1016/j.pep.2023.106245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/23/2023] [Accepted: 02/06/2023] [Indexed: 02/18/2023]
Abstract
Human bone morphogenetic protein 2 (hBMP-2) plays a leading role in the process of osteogenesis and is one of the key components of osteoplastic materials, ensuring their high osteoinduction. In order to obtain a homodimeric form hBMP-2 using the E. coli expression system, a number of problems associated with refolding in vitro and purification from monomer and oligomeric forms must be solved. The developed method for co-expression of the target protein with chaperone proteins makes it possible to obtain the biologically active homodimeric form of hBMP-2 in vivo. Purification with simple ion-exchange sorbents without the use of denaturing reagents affecting the structure of the protein molecule provides a chromatographic purity of the product of at least 97%. The expressed hBMP-2 was identified by Western blotting and the LC-ESI-TOF mass spectrometry confirmed its molecular weight of 26052.72 Da. Circular dichroism spectroscopy showed that recombinant hBMP-2 has a native secondary structure.
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Affiliation(s)
- Dmitry D Lykoshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Maria A Kostromina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Veronika R Azmukova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Roman S Esipov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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3
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Zayats EA, Fateev IV, Kostromina MA, Abramchik YA, Lykoshin DD, Yurovskaya DO, Timofeev VI, Berzina MY, Eletskaya BZ, Konstantinova ID, Esipov RS. Rational Mutagenesis in the Lid Domain of Ribokinase from E. coli Results in an Order of Magnitude Increase in Activity towards D-arabinose. Int J Mol Sci 2022; 23:ijms232012540. [PMID: 36293391 PMCID: PMC9604405 DOI: 10.3390/ijms232012540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/12/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
Development of efficient approaches for the production of medically important nucleosides is a highly relevant challenge for biotechnology. In particular, cascade synthesis of arabinosides would allow relatively easy production of various cytostatic and antiviral drugs. However, the biocatalyst necessary for this approach, ribokinase from Escherichia coli (EcoRK), has a very low activity towards D-arabinose, making the synthesis using the state-of-art native enzyme technologically unfeasible. Here, we report the results of our enzyme design project, dedicated to engineering a mutant form of EcoRK with elevated activity towards arabinose. Analysis of the active site structure has allowed us to hypothesize the reasons behind the low EcoRK activity towards arabinose and select feasible mutations. Enzyme assay and kinetic studies have shown that the A98G mutation has caused a large 15-fold increase in kcat and 1.5-fold decrease in KM for arabinose phosphorylation. As a proof of concept, we have performed the cascade synthesis of 2-chloroadenine arabinoside utilizing the A98G mutant with 10-fold lower amount of enzyme compared to the wild type without any loss of synthesis efficiency. Our results are valuable both for the development of new technologies of synthesis of modified nucleosides and providing insight into the structural reasons behind EcoRK substrate specificity.
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Timofeev VI, Fateev IV, Kostromina MA, Abramchik YA, Konstantinova ID, Volkov VV, Lykoshin DD, Mikheeva OO, Muravieva TI, Esipov RS, Kuranova IP. The comparative analysis of the properties and structures of purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27. J Biomol Struct Dyn 2020; 40:3626-3641. [PMID: 33225840 DOI: 10.1080/07391102.2020.1848628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Two recombinant purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27 encoded by genes TT_C1070 (TthPNPI) and TT_C0194 (TthPNPII) were purified and characterized. The comparative analysis of their sequences, molecular weight, enzymes specificity and kinetics of the catalyzed reaction were realized. As a result, it was determined that the TthPNPI is specific to guanosine while the TthPNPII to adenosine. According to the results of the size exclusion chromatography and SAXS study both enzymes are hexameric molecules. Based on the sequence alignment with homologous purine nucleoside phosphorylases (PNPs), Asn was identified as a purine base recognizing residue in the active site of TthPNPI and Asp in TthPNPII. The three-dimensional structure of TthPNPII was solved at 2.5 Å resolution by molecular replacement method using crystals grown in microgravity. Position of phosphate in the active site cavity is located. The possible arrangement of adenosine and guanosine in TthPNPII active site cavity is considered using superposition with the structures of homologous trimeric and hexameric PNPs complexed with corresponding substrates. The peculiarities of oligomeric structure of TthPNPII in comparison with homologous PNPs are described. It is shown that two trimeric molecules of TthPNPII in the asymmetric part of the unit cell are connected by three two-fold axis into a hexamer with 32-point symmetry. This type of hexameric structure of PNP is found for the first time. The interface area between the subunits in trimeric molecule and between the trimers in TthPNPII hexamer is described.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation
| | - Ilya V Fateev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria A Kostromina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yuliya A Abramchik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Irina D Konstantinova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir V Volkov
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry D Lykoshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Olga O Mikheeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana I Muravieva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Roman S Esipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Inna P Kuranova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation
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Eletskaya BZ, Gruzdev DA, Krasnov VP, Levit GL, Kostromina MA, Paramonov AS, Kayushin AL, Muzyka IS, Muravyova TI, Esipov RS, Andronova VL, Galegov GA, Charushin VN, Miroshnikov AI, Konstantinova ID. Enzymatic synthesis of novel purine nucleosides bearing a chiral benzoxazine fragment. Chem Biol Drug Des 2019; 93:605-616. [PMID: 30561886 DOI: 10.1111/cbdd.13458] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/28/2018] [Accepted: 12/07/2018] [Indexed: 12/01/2022]
Abstract
A series of ribo- and deoxyribonucleosides bearing 2-aminopurine as a nucleobase with 7,8-difluoro- 3,4-dihydro-3-methyl-2H-[1,4]benzoxazine (conjugated directly or through an aminohexanoyl spacer) was synthesized using an enzymatic transglycosylation reaction. Nucleosides 3-6 were resistant to deamination under action of adenosine deaminase (ADA) Escherichia coli and ADA from calf intestine. The antiviral activity of the modified nucleosides was evaluated against herpes simplex virus type 1 (HSV-1, strain L2). It has been shown that at sub-toxic concentrations, nucleoside (S)-4-[2-amino-9-(β-D-ribofuranosyl)-purin-6-yl]-7,8-difluoro-3,4-dihydro-3-methyl-2H-[1,4]benzoxazine exhibit significant antiviral activity (SI > 32) on the model of HSV-1 in vitro, including an acyclovir-resistant virus strain (HSV-1, strain L2/R).
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Affiliation(s)
- Barbara Z Eletskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A Gruzdev
- Postovsky Institute of Organic Synthesis, Russian Academy of Sciences (Ural Branch), Ekaterinburg, Russia
| | - Victor P Krasnov
- Postovsky Institute of Organic Synthesis, Russian Academy of Sciences (Ural Branch), Ekaterinburg, Russia
| | - Galina L Levit
- Postovsky Institute of Organic Synthesis, Russian Academy of Sciences (Ural Branch), Ekaterinburg, Russia
| | - Maria A Kostromina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Paramonov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexei L Kayushin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Inessa S Muzyka
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatyana I Muravyova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Roman S Esipov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Valeria L Andronova
- Ivanovsky Institute of Virology (Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation), Moscow, Russia
| | - Georgiy A Galegov
- Ivanovsky Institute of Virology (Gamaleya Research Center of Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation), Moscow, Russia
| | - Valery N Charushin
- Postovsky Institute of Organic Synthesis, Russian Academy of Sciences (Ural Branch), Ekaterinburg, Russia.,Ural Federal University named after the first President of Russia B.N. Yeltsin, Ekaterinburg, Russia
| | - Anatoly I Miroshnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Irina D Konstantinova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Fateev IV, Sinitsina EV, Bikanasova AU, Kostromina MA, Tuzova ES, Esipova LV, Muravyova TI, Kayushin AL, Konstantinova ID, Esipov RS. Thermophilic phosphoribosyltransferases Thermus thermophilus HB27 in nucleotide synthesis. Beilstein J Org Chem 2018; 14:3098-3105. [PMID: 30643587 PMCID: PMC6317416 DOI: 10.3762/bjoc.14.289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/27/2018] [Indexed: 11/23/2022] Open
Abstract
Phosphoribosyltransferases are the tools that allow the synthesis of nucleotide analogues using multi-enzymatic cascades. The recombinant adenine phosphoribosyltransferase (TthAPRT) and hypoxanthine phosphoribosyltransferase (TthHPRT) from Thermus thermophilus HB27 were expressed in E.coli strains and purified by chromatographic methods with yields of 10-13 mg per liter of culture. The activity dependence of TthAPRT and TthHPRT on different factors was investigated along with the substrate specificity towards different heterocyclic bases. The kinetic parameters for TthHPRT with natural substrates were determined. Two nucleotides were synthesized: 9-(β-D-ribofuranosyl)-2-chloroadenine 5'-monophosphate (2-Сl-AMP) using TthAPRT and 1-(β-D-ribofuranosyl)pyrazolo[3,4-d]pyrimidine-4-one 5'-monophosphate (Allop-MP) using TthНPRT.
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Affiliation(s)
- Ilja V Fateev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya Str., 16/10, Moscow, GSP-7, 117997, Russia
| | - Ekaterina V Sinitsina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya Str., 16/10, Moscow, GSP-7, 117997, Russia
| | - Aiguzel U Bikanasova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya Str., 16/10, Moscow, GSP-7, 117997, Russia
| | - Maria A Kostromina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya Str., 16/10, Moscow, GSP-7, 117997, Russia
| | - Elena S Tuzova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya Str., 16/10, Moscow, GSP-7, 117997, Russia
| | - Larisa V Esipova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya Str., 16/10, Moscow, GSP-7, 117997, Russia
| | - Tatiana I Muravyova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya Str., 16/10, Moscow, GSP-7, 117997, Russia
| | - Alexei L Kayushin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya Str., 16/10, Moscow, GSP-7, 117997, Russia
| | - Irina D Konstantinova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya Str., 16/10, Moscow, GSP-7, 117997, Russia
| | - Roman S Esipov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya Str., 16/10, Moscow, GSP-7, 117997, Russia
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Zayats EA, Timofeev VI, Kostromina MA, Esipov RS. An explanation for the narrow carbohydrate substrate specificity of adenine phosphoribosyltransferase from Thermus thermophilus from the model of the enzyme, substrate, and magnesium cation cofactor complex. J Biomol Struct Dyn 2018; 37:4460-4464. [PMID: 30451097 DOI: 10.1080/07391102.2018.1550020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Evgeniy A Zayats
- Shemyakin & Ovchinnikov Institute of Bioorganic chemistry RAS , Moscow , Russian Federation
| | - Vladimir I Timofeev
- Shemyakin & Ovchinnikov Institute of Bioorganic chemistry RAS , Moscow , Russian Federation.,Federal Scientific Research Center "Crystallography and Photonics" RAS , Moscow , Russian Federation.,National Research Centre "Kurchatov Institute ," Moscow , Russian Federation
| | - Maria A Kostromina
- Shemyakin & Ovchinnikov Institute of Bioorganic chemistry RAS , Moscow , Russian Federation
| | - Roman S Esipov
- Shemyakin & Ovchinnikov Institute of Bioorganic chemistry RAS , Moscow , Russian Federation
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8
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Timofeev VI, Zhukhlistova NE, Abramchik YA, Fateev II, Kostromina MA, Muravieva TI, Esipov RS, Kuranova IP. Crystal structure of Escherichia coli purine nucleoside phosphorylase in complex with 7-deazahypoxanthine. Acta Crystallogr F Struct Biol Commun 2018; 74:355-362. [PMID: 29870020 PMCID: PMC5987744 DOI: 10.1107/s2053230x18006337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/25/2018] [Indexed: 11/10/2022] Open
Abstract
Purine nucleoside phosphorylases (EC 2.4.2.1; PNPs) reversibly catalyze the phosphorolytic cleavage of glycosidic bonds in purine nucleosides to generate ribose 1-phosphate and a free purine base, and are key enzymes in the salvage pathway of purine biosynthesis. They also catalyze the transfer of pentosyl groups between purine bases (the transglycosylation reaction) and are widely used for the synthesis of biologically important analogues of natural nucleosides, including a number of anticancer and antiviral drugs. Potent inhibitors of PNPs are used in chemotherapeutic applications. The detailed study of the binding of purine bases and their derivatives in the active site of PNPs is of particular interest in order to understand the mechanism of enzyme action and for the development of new enzyme inhibitors. Here, it is shown that 7-deazahypoxanthine (7DHX) is a noncompetitive inhibitor of the phosphorolysis of inosine by recombinant Escherichia coli PNP (EcPNP) with an inhibition constant Ki of 0.13 mM. A crystal of EcPNP in complex with 7DHX was obtained in microgravity by the counter-diffusion technique and the three-dimensional structure of the EcPNP-7DHX complex was solved by molecular replacement at 2.51 Å resolution using an X-ray data set collected at the SPring-8 synchrotron-radiation facility, Japan. The crystals belonged to space group P6122, with unit-cell parameters a = b = 120.370, c = 238.971 Å, and contained three subunits of the hexameric enzyme molecule in the asymmetric unit. The 7DHX molecule was located with full occupancy in the active site of each of the three crystallographically independent enzyme subunits. The position of 7DHX overlapped with the positions occupied by purine bases in similar PNP complexes. However, the orientation of the 7DHX molecule differs from those of other bases: it is rotated by ∼180° relative to other bases. The peculiarities of the arrangement of 7DHX in the EcPNP active site are discussed.
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Affiliation(s)
- Vladimir I. Timofeev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
- Kurchatov Complex of NBICS-Technologies, National Research Center ‘Kurchatov Institute’, Akad. Kurchatova Square 1, Moscow 123182, Russian Federation
| | - Nadezhda E. Zhukhlistova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
| | - Yuliya A. Abramchik
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Ilya I. Fateev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Maria A. Kostromina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Tatiana I. Muravieva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Roman S. Esipov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Inna P. Kuranova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
- Kurchatov Complex of NBICS-Technologies, National Research Center ‘Kurchatov Institute’, Akad. Kurchatova Square 1, Moscow 123182, Russian Federation
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9
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Esipov RS, Makarov DA, Stepanenko VN, Kostromina MA, Muravyova TI, Andreev YA, Dyachenko IA, Kozlov SA, Grishin EV. Pilot production of the recombinant peptide toxin of Heteractis crispa as a potential analgesic by intein-mediated technology. Protein Expr Purif 2017; 145:71-76. [PMID: 29289634 DOI: 10.1016/j.pep.2017.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/22/2017] [Accepted: 12/24/2017] [Indexed: 10/18/2022]
Abstract
APHC3 is an analgesic polypeptide that was found in the sea anemone (Heteractis crispa), and contains 56 amino acid residues. This polypeptide is of interest for the development of medications for diseases, associated with inflammatory or neuropathological processes, as well as its use as an analgesic. This work presents an innovative biotechnological method for APHC3 production. We have constructed a recombinant plasmid intended for biosynthesizing the fusion protein consisting of a chitin-binding domain, DnaB mini-intein from Synechocystis sp. capable of undergoing pH-dependent self-cleavage, and the target peptide. In the process of biosynthesis the fusion protein aggregates and forms the inclusion bodies that are welcomed since APHC3 is a cytotoxic peptide. The target peptide recovery process developed by us involves 3 chromatographic steps. The method developed by us enables to produce 940 mg of the recombinant APHC3 from 100 g of the inclusion bodies. The method is straightforward to implement and scale up. The recombinant APHC3 activity and effectiveness as an analgesic was proved by animal testing.
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Affiliation(s)
- Roman S Esipov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russian Federation.
| | - Dmitry A Makarov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russian Federation.
| | - Vasily N Stepanenko
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russian Federation.
| | - Maria A Kostromina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russian Federation.
| | - Tatyana I Muravyova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russian Federation.
| | - Yaroslav A Andreev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russian Federation.
| | - Igor A Dyachenko
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russian Federation.
| | - Sergey A Kozlov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russian Federation.
| | - Evgeny V Grishin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, GSP-7, Miklukho-Maklaya str., 16/10, 117997, Moscow, Russian Federation.
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10
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Timofeev VI, Sinitsyna EV, Kostromina MA, Muravieva TI, Makarov DA, Mikheeva OO, Kuranova IP, Esipov RS. Crystal structure of recombinant phosphoribosylpyrophosphate synthetase 2 from Thermus thermophilus HB27 complexed with ADP and sulfate ions. Acta Crystallogr F Struct Biol Commun 2017; 73:369-375. [PMID: 28580926 PMCID: PMC5458395 DOI: 10.1107/s2053230x17007488] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 05/20/2017] [Indexed: 11/10/2022] Open
Abstract
Phosphoribosylpyrophosphate synthetase (PRPPS) from the thermophilic bacterial strain Thermus thermophilus HB27 catalyzes the synthesis of phosphoribosylpyrophosphate from ribose 5-phosphate and ATP, and belongs to the class I PRPPSs. The three-dimensional structure of the recombinant enzyme was solved at 2.2 Å resolution using crystals grown in microgravity from protein solution containing ATP, magnesium and sulfate ions. An ADP molecule was located in the active site of each subunit of the hexameric enzyme molecule and sulfate ions were located in both the active and allosteric sites. It was found that the catalytic loop that restricts the active-site area and is usually missing from the electron-density map of class I PRPPSs adopts different conformations in three independent subunits in T. thermophilus PRPPS. A closed conformation of the active site was found in one of subunits where the highly ordered catalytic β-hairpin delivers the Lys and Arg residues that are essential for activity directly to the ADP molecule, which occupies the ATP-binding site. A comparison of the conformations of the catalytic loop in the three independent subunits reveals a possible mode of transition from the open to the closed state of the active site during the course of the catalyzed reaction.
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Affiliation(s)
- Vladimir I. Timofeev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
- National Research Center ‘Kurchatov Institute’, Kurchatov Complex of NBICS-Technologies, Akad. Kurchatova Square 1, Moscow 123182, Russian Federation
| | - Ekaterina V. Sinitsyna
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Maria A. Kostromina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Tatiana I. Muravieva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Dmitry A. Makarov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Olga O. Mikheeva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Inna P. Kuranova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
- National Research Center ‘Kurchatov Institute’, Kurchatov Complex of NBICS-Technologies, Akad. Kurchatova Square 1, Moscow 123182, Russian Federation
| | - Roman S. Esipov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
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11
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Kostromina MA, Esipov RS, Miroshnikov AI. [Biotechnological production of recombinant analogs of hirudin-1 from Hirudo medicinalis]. Bioorg Khim 2012; 38:166-76. [PMID: 22792720 DOI: 10.1134/s1068162012020057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Hirudin-1 is a highly selective inhibitor of thrombin secreted by salivary glands of the medicinal leech Hirudo medicinalis. This direct anticoagulant is used for the treatment and prevention of disorders in blood coagulation system. Apart from the existing recombinant analog of hirudin-1 (63-desulfatohirudin-1, desirudin) its modified analogs possessing higher activity and stability are of medical value. In this study artificial genes of hirudin and two its analogs (hirudin-1, [Leu1, Thr2]-hirudin-1 and [Leu1, Thr2]-hirudin-1/3) were synthesized and cloned in an expression vector pTWIN1 in frame with the gene of mini-intein SspDnaB from Synechocystis sp. Producing strains of the corresponding fusion proteins were constructed using E. coli strain ER2566. Biotechnological schemes for the production of 63-desulfatohirudin-1 and its analogs were developed. The scheme includes the following stages: isolation of the fusion protein after the desintegration of the cell biomass, refolding of the target peptide within the fusion protein, pH-inducible cleavage of the fusion protein, and chromatographic purification of the target product. Antithrombotic activity of the obtained peptides was determined by a standard amidolytic assay. The developed methods for the production of 63-desulfatohirudin-1, [Leu1, Thr2]-desulfatohirudin-1 [Leu1, Thr2]-desulfatohirudin-1/3 allowed to obtain these peptides with high yields (14, 25 and 24 mg per liter of cell culture respectively) and high activity (13423, 33333 and 19802 ATU/mg respectively).
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