Targeted drug delivery to the thrombus by fusing streptokinase with a fibrin-binding peptide (CREKA): an in silico study

References

• Ząbczyk M, Ariëns RAS, Undas A. Fibrin clot properties in cardiovascular disease: from basic mechanisms to clinical practice. Cardiovasc. Res. 2023 Mar 17;119(1):94–111.
   PubMed Web of Science ®Google Scholar
• Kwaan HC. The role of fibrinolytic system in health and disease. Inter. J. Mol. Sci. 2022 May 9;23(9):5262.
   PubMed Web of Science ®Google Scholar
• Mican J, Toul M, Bednar D et al. Structural biology and protein engineering of thrombolytics. Comput. Struct. Biotechnol. J. 2019;17:917–938.
   PubMed Web of Science ®Google Scholar
• Wang X, Tang J, Hunter B et al. Crystal structure of streptokinase β-domain. FEBS Lett. 1999;459(1):85–89.
   PubMed Web of Science ®Google Scholar
• Zia MA. Streptokinase: an efficient enzyme in cardiac medicine. Protein Pept. Lett. 2020;27(2):111–119.
   PubMed Web of Science ®Google Scholar
• Edwards Z, Nagalli S. Streptokinase. StatPearls. Treasure Island (FL): StatPearls Publishing Copyright © 2023, StatPearls Publishing LLC; 2023.
   Google Scholar
• Li S, Zhang K, Ma Z et al. Biomimetic nanoplatelets to target delivery hirudin for site-specific photothermal/photodynamic thrombolysis and preventing venous thrombus formation. Small (Weinheim an der Bergstrasse, Germany). 2022 Dec;18(51):e2203184.
   PubMed Web of Science ®Google Scholar
• Deng J, Mei H, Shi W et al. Recombinant tissue plasminogen activator-conjugated nanoparticles effectively targets thrombolysis in a rat model of middle cerebral artery occlusion. Curr. Med. Sci. 2018 Jun;38(3):427–435.
   PubMed Web of Science ®Google Scholar
• Simberg D, Duza T, Park JH et al. Biomimetic amplification of nanoparticle homing to tumors. Proc. Natl. Acad. Sci. USA 2007;104(3):932–936.
   PubMed Web of Science ®Google Scholar
• Zhang N, Ru B, Hu J et al. Recent advances of CREKA peptide-based nanoplatforms in biomedical applications. J. Nanobiotechnol. 2023 Mar 3;21(1):77.
   PubMed Web of Science ®Google Scholar
• Okur AC, Erkoc P, Kizilel S. Targeting cancer cells via tumor-homing peptide CREKA functional PEG nanoparticles. Colloid. Surf. B, Biointerf. 2016 Nov 1;147:191–200.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Wang L, Yu S et al. Synthesis and preclinical evaluation of the fibrin-binding cyclic peptide (18)F-iCREKA: comparison with its contrasted linear peptide. Contrast Media Mol. Imag. 2019;2019:6315954–6315954.
   PubMedGoogle Scholar
• Mundada LV, Prorok M, DeFord ME et al. Structure-function analysis of the streptokinase amino terminus (residues 1–59). J. Biol. Chem. 2003/07/04/;278(27):24421–24427.
   PubMed Web of Science ®Google Scholar
• Kunamneni A, Abdelghani TT, Ellaiah P. Streptokinase--the drug of choice for thrombolytic therapy. J. Thromb. Thrombolys. 2007 Feb;23(1):9–23.
   PubMed Web of Science ®Google Scholar
• Kazemi F, Arab SS, Mohajel N et al. Computational simulations assessment of mutations impact on streptokinase (SK) from a group G streptococci with enhanced activity - insights into the functional roles of structural dynamics flexibility of SK and stabilization of SK-μplasmin catalytic complex. J. Biomol. Struct. Dynam. 2019 May;37(8):1944–1955.
   PubMed Web of Science ®Google Scholar
• Nihalani D, Sahni G. Streptokinase contains two independent plasminogen-binding sites. Biochem. Biophys. Res. Commun. 1995 Dec 26;217(3):1245–1254.
   PubMed Web of Science ®Google Scholar
• Shi GY, Chang BI, Chen SM et al. Function of streptokinase fragments in plasminogen activation. Biochem. J. 1994 Nov 15;304(Pt 1):235–241.
   PubMedGoogle Scholar
• Nihalani D, Raghava GP, Sahni G. Mapping of the plasminogen binding site of streptokinase with short synthetic peptides. Protein Sci. 1997 Jun;6(6):1284–1292.
   PubMed Web of Science ®Google Scholar
• Tharp AC, Laha M, Panizzi P et al. Plasminogen substrate recognition by the streptokinase-plasminogen catalytic complex is facilitated by Arg253, Lys256, and Lys257 in the streptokinase β-domain and kringle 5 of the substrate. J. Biol. Chem. 2009/07/17/;284(29):19511–19521.
   PubMed Web of Science ®Google Scholar
• Aneja R, Datt M, Yadav S et al. Multiple exosites distributed across the three domains of streptokinase co-operate to generate high catalytic rates in the streptokinase–plasmin activator complex. Biochemistry 2013/12/10;52(49):8957–8968.
   PubMed Web of Science ®Google Scholar
• Wu D-H, Shi G-Y, Chuang W-J et al. Coiled coil region of streptokinase γ-domain is essential for plasminogen activation. J. Biol. Chem. 2001;276(18):15025–15033.
   PubMed Web of Science ®Google Scholar
• Yadav S, Aneja R, Kumar P et al. Identification through combinatorial random and rational mutagenesis of a substrate-interacting exosite in the gamma domain of streptokinase. J. Biol. Chem. 2011 Feb 25;286(8):6458–6469.
   PubMed Web of Science ®Google Scholar
• Verhamme IM, Bock PE. Rapid binding of plasminogen to streptokinase in a catalytic complex reveals a three-step mechanism. J. Biol. Chem. 2014 Oct 3;289(40):28006–28018.
   PubMed Web of Science ®Google Scholar
• Pierce BG, Wiehe K, Hwang H et al. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics (Oxford, England). 2014 Jun 15;30(12):1771–1773.
   PubMed Web of Science ®Google Scholar
• Vreven T, Pierce BG, Hwang H et al. Performance of ZDOCK in CAPRI rounds 20–26. Proteins 2013 Dec;81(12):2175–2182.
   PubMed Web of Science ®Google Scholar
• Vreven T, Pierce BG, Borrman TM et al. Performance of ZDOCK and IRAD in CAPRI rounds 28–34. Proteins 2017 Mar;85(3):408–416.
   PubMed Web of Science ®Google Scholar
• Vreven T, Vangaveti S, Borrman TM et al. Performance of ZDOCK and IRAD in CAPRI rounds 39–45. Proteins 2020 Aug;88(8):1050–1054.
   PubMed Web of Science ®Google Scholar
• Chen J, Song Y, Huang Z et al. Modification with CREKA improves cell retention in a rat model of myocardial ischemia reperfusion. Stem cells (Dayton, Ohio). 2019 May;37(5):663–676.
   PubMed Web of Science ®Google Scholar
• Cheng Z, Jin Y, Li J et al. Fibronectin-targeting and metalloproteinase-activatable smart imaging probe for fluorescence imaging and image-guided surgery of breast cancer. J. Nanobiotechnol. 2023 Mar 28;21(1):112.
   PubMed Web of Science ®Google Scholar
• P00779 · STRP_STREQ amino acid sequence. [ cited 2023 Feb 1]. Available from: https://www.uniprot.org/uniprotkb/P00779/entry
   Google Scholar
• Kringelum JV, Lundegaard C, Lund O et al. Reliable B cell epitope predictions: impacts of method development and improved benchmarking. PLoS Computat. Biol. 2012;8(12):e1002829.
   PubMed Web of Science ®Google Scholar
• Protparam tool help bar. [ cited 2023 Mar 20]. Available from: https://web.expasy.org/protparam/protparam-doc.html#:∼:text=Using%20these%20weight%20values%20it%20is%20possible%20to,value%20for%20the%20dipeptide%20starting%20in%20position%20i
   Google Scholar
• Oluwagbemi OO, Oladipo EK, Dairo EO et al. Computational construction of a glycoprotein multi-epitope subunit vaccine candidate for old and new South-African SARS-CoV-2 virus strains. Informat. Med. Unlock. 2022;28:100845.
   PubMedGoogle Scholar
• Asghari A, Kordi B, Maleki B et al. Neospora caninum SRS2 protein: essential vaccination targets and biochemical features for next-generation vaccine design. BioMed. Res. Int. 2022;2022:7070144.
   PubMed Web of Science ®Google Scholar
• Aarthy M, Singh SK. Chapter 28 - Envisaging the conformational space of proteins by coupling machine learning and molecular dynamics. In: Tripathi T, Dubey VK, editors. Advances in protein molecular and structural biology methods. Cambridge, MA, USA: Academic Press; 2022. p. 467–475.
   Google Scholar
• Chamizo-González F, Gordillo B, Heredia FJ. Elucidation of the 3D structure of grape seed 7S globulin and its interaction with malvidin 3-glucoside: a molecular modeling approach. Food Chem. 2021 2021/06/15/;347:129014.
   PubMed Web of Science ®Google Scholar
• McGuffin LJ, Aldowsari FMF, Alharbi SMA et al. ModFOLD8: accurate global and local quality estimates for 3D protein models. Nucleic Acids Res. 2021 Jul 2;49(W1):W425–w430.
   PubMed Web of Science ®Google Scholar
• Yun S, Guy HR. Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations. J. Mol. Graph. Model. 2011 Feb;29(5):663–675.
   PubMed Web of Science ®Google Scholar
• Sitthiyotha T, Klaewkla M, Krusong K et al. Computational design of Lactobacillus Acidophilus α-L-rhamnosidase to increase its structural stability. PLoS One 2022;17(5):e0268953.
   PubMed Web of Science ®Google Scholar
• De Vita S, Chini MG, Bifulco G et al. Insights into the ligand binding to bromodomain-containing protein 9(BRD9), a guide to the selection of potential binders by computational methods. Molecules (Basel, Switzerland). 2021 Nov 27;26(23):7192.
   PubMed Web of Science ®Google Scholar