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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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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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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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