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Anticoagulant activity screening of an in-house database of natural compounds for discovering novel selective factor Xa inhibitors; a combined in silico and in vitro approach

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Abstract

Traditional edible natural products enclose a wealth of anticoagulants that can be prospected for new selective factor Xa inhibitors. Unlike multitargeted anticoagulants, selective factor Xa inhibitors effectively block coagulation cascade with a broader therapeutic window. In the present study, an in-house database comprises 3D structures of 1571 compounds from 26 natural products previously reported to enhance the bleeding tendency was compiled. Virtual screening (VS) of the constructed database to discover active FXa inhibitors was performed using sequential structure-based VS by Glide extra precision docking followed by ligand-based VS through pharmacophore modeling and 3D-QSAR. The implemented approach provoked liquorice, trifolium and olive as candidates for chromogenic in vitro FXa inhibitory assay with IC50 values of 0.363, 0.729, and 0.866 mg/mL, respectively. Evaluation of liquorice solvent fractions revealed that ethyl acetate fraction produced 97.93 ± 0.019% inhibition of FXa. The adopted integrated strategy can be implemented for isolation of potent, selective nature-based FXa inhibitors.

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References

  • Acharya C, Coop A, Polli JE, MacKerell AD (2011) Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach. Curr Comput Aided Drug Des 7(1):10–22

    CAS  PubMed  PubMed Central  Google Scholar 

  • Al-Awwadi NAJ (2010) Effects of Achillea Santolina extracts and fractions on human platelet aggregation in vitro and on rat arteriovenous shunt thrombosis in vivo. Thi-Qar Med J 4(3):131–141

    Google Scholar 

  • Ali AH, Abdul-Azeez LA, Humood JK, Ali ZA, Helal ZH, Wahab FL (2016) The Effect of Ethanolic Extract of Hibiscus sabdariffa on some Physiological and Antioxidant Parameters in Female Rabbits. J Anim Health Prod 4(2):37–41

    Google Scholar 

  • Amrani S, Harnafi H, Gadi D, Mekhfi H, Legssyer A, Aziz M, Martin-Nizard F, Bosca L (2009) Vasorelaxant and anti-platelet aggregation effects of aqueous Ocimum basilicum extract. J Ethnopharmacol 125(1):157–162

    PubMed  Google Scholar 

  • Aurell L, Friberger P, Karlsson G, Claeson G (1977) A new sensitive and highly specific chromogenic peptide substrate for Factor Xa. Thrombosis Res 11(5):595–609

    CAS  Google Scholar 

  • Bielecki S, Lee D, Hamad B (2018) The market for oral anticoagulants. Nat Rev Drug Discov 17:617

    CAS  PubMed  Google Scholar 

  • Bijak M, Ponczek MB, Nowak P (2014) Polyphenol compounds belonging to flavonoids inhibit activity of coagulation factor X. Int J Biol Macromol 65:129–135

    CAS  PubMed  Google Scholar 

  • Booth NL, Nikolic D, van Breemen RB, Geller SE, Banuvar S, Shulman LP, Farnsworth NR (2004) Confusion regarding anticoagulant coumarins in dietary supplements. Clin Pharm Ther 76(6):511–516

    CAS  Google Scholar 

  • Brandstetter H, Kuhne A, Bode W, Huber R, von der Saal W, Wirthensohn K, Engh RA (1996) X-ray structure of active site-inhibited clotting factor Xa. Implications for drug design and substrate recognition. J Biol Chem 271(47):29988–29992

    CAS  PubMed  Google Scholar 

  • Choudhari PB, Bhatia MS (2012) 3D QSAR, docking studies, and pharmacophore modeling of selected factor Xa inhibitors. Med Chem Res 21(7):1427–1432

    CAS  Google Scholar 

  • Cordier W, Steenkamp V (2012) Herbal remedies affecting coagulation: a review. Pharm Biol 50(4):443–452

    CAS  PubMed  Google Scholar 

  • Correia-da-Silva M, Sousa E, Duarte B, Marques F, Carvalho F, Cunha-Ribeiro LM, Pinto MM (2010) Flavonoids with an oligopolysulfated moiety: a new class of anticoagulant agents. J Med Chem 54(1):95–106

    PubMed  Google Scholar 

  • Cross S, Baroni M, Carosati E, Benedetti P, Clementi S (2010) FLAP: GRID molecular interaction fields in virtual screening. validation using the DUD data set. J Chem Inf Modeling 50(8):1442–1450

    CAS  Google Scholar 

  • Dawood HM, Ibrahim RS, Shawky E, Hammoda HM, Metwally AM (2018) Integrated in silico-in vitro strategy for screening of some traditional Egyptian plants for human aromatase inhibitors. J Ethnopharmacol 224:359–372

    CAS  PubMed  Google Scholar 

  • De Caterina R, Husted S, Wallentin L, Andreotti F, Arnesen H, Bachmann F, Baigent C, Huber K, Jespersen J, Kristensen SD, Lip GY, Morais J, Rasmussen LH, Siegbahn A, Verheugt FW, Weitz JI (2013) General mechanisms of coagulation and targets of anticoagulants (Section I). Position Paper of the ESC Working Group on Thrombosis–Task Force on Anticoagulants in Heart Disease. Thromb Haemost 109(4):569–579

    PubMed  Google Scholar 

  • Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA (2006) PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des 20(10–11):647–671

    CAS  PubMed  Google Scholar 

  • DJ S (2015) Xabans as direct factor X. J Bioanal Biomedicine 7(1):01

    Google Scholar 

  • Dong-juan L, Jia-fu W, Wei L (2006) Inhibitive effects of flavone from propolis on platelet activity in flowing blood. Chin J Clin Rehabil 10(47):174

  • Dub AM, Dugani AM (2013) Antithrombotic effect of repeated doses of the ethanolic extract of local olive (L.) leaves in rabbits. Libyan J Med 8(1):20947

    PubMed  Google Scholar 

  • Dureja H, Kumar V, Gupta S, Madan AK (2007) Topochemical models for the prediction of lipophilicity of 1,3-disubstituted propan-2-one analogs. J Theor Computational Chem 06(03):435–448

    CAS  Google Scholar 

  • Ewing W, Becker M, Manetta V, Davis R, Pauls H, Mason H, Choi-Sledeski Y, Green D, Cha D, Spada A, Cheney D, Mason J, Maignan S, Guilloteau J, Brown K, Colussi D, Bentley R, Bostwick J, Kasiewski C, Chu V (1999) Design and structure−activity relationships of potent and selective inhibitors of blood coagulation factor Xa. J Med Chem 42:3571–3557

    Google Scholar 

  • Fuentes E, Alarcón M, Fuentes A, Carrasco G, Palomo I (2014) A Novel Role of Eruca sativa Mill. (Rocket) Extract: Antiplatelet (NF-κB Inhibition) and Antithrombotic Activities. Nutrients 6(12):5839–5852

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP (2012) ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 40:D1100–D1107

    CAS  Google Scholar 

  • Gilani AH, Rahman AU (2005) Trends in ethnopharmacology. J Ethnopharmacol 100(1–2):43–49

    PubMed  Google Scholar 

  • Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47(7):1750–1759

    CAS  PubMed  Google Scholar 

  • Harder S, Graff J (2013) Novel oral anticoagulants: clinical pharmacology, indications and practical considerations. Eur J Clin Pharmacol 69(9):1617–1633

    CAS  PubMed  Google Scholar 

  • Jiang L, Wang Q, Shen S, Xiao T, Li Y (2014) Discovery of glycyrrhetinic acid as an orally active, direct inhibitor of blood coagulation factor xa. Thrombosis Res 133(3):501–506

    CAS  Google Scholar 

  • Kaur P, Sharma V, Kumar V (2012) Pharmacophore modelling and 3D-QSAR studies on N(3)-phenylpyrazinones as corticotropin-releasing factor 1 receptor antagonists. Int J Med Chem 2012:452325

    PubMed  PubMed Central  Google Scholar 

  • Kellenberger E, Rodrigo J, Muller P, Rognan D (2004) Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins 57(2):225–242

    CAS  PubMed  Google Scholar 

  • Kirchmair J, Markt P, Distinto S, Wolber G, Langer T (2008) Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection–what can we learn from earlier mistakes? J Comput Aided Mol Des 22(3–4):213–228

    CAS  PubMed  Google Scholar 

  • Kolodziejczyk-Czepas J, Sieradzka M, Wachowicz B, Nowak P, Oleszek W, Stochmal A (2016) The anti-adhesive and anti-aggregatory effects of phenolics from Trifolium species in vitro. Mol Cell Biochem 412(1):155–164

    CAS  PubMed  Google Scholar 

  • Kolodziejczyk-Czepas J, Sieradzka M, Moniuszko-Szajwaj B, Nowak P, Oleszek W, Stochmal A (2018) Phenolic fractions from nine Trifolium species modulate the coagulant properties of blood plasma in vitro without cytotoxicity towards blood cells. J Pharm Pharmacol 70(3):413–425

    CAS  PubMed  Google Scholar 

  • Ku SK, Kim TH, Bae JS (2013) Anticoagulant activities of persicarin and isorhamnetin. Vasc Pharm 58(4):272–279

    CAS  Google Scholar 

  • Lagarde N, Zagury J-F, Montes M (2015) Benchmarking data sets for the evaluation of virtual ligand screening methods: review and perspectives. J Chem Inf Modeling 55(7):1297–1307

    CAS  Google Scholar 

  • Lagunin AA, Goel RK, Gawande DY, Pahwa P, Gloriozova TA, Dmitriev AV, Ivanov SM, Rudik AV, Konova VI, Pogodin PV, Druzhilovsky DS, Poroikov VV (2014) Chemo- and bioinformatics resources for in silico drug discovery from medicinal plants beyond their traditional use: a critical review. Nat Prod Rep. 31(11):1585–1611

    CAS  PubMed  Google Scholar 

  • Laux V, Perzborn E, Heitmeier S, von Degenfeld G, Dittrich-Wengenroth E, Buchmuller A, Gerdes C, Misselwitz F (2009) Direct inhibitors of coagulation proteins - the end of the heparin and low-molecular-weight heparin era for anticoagulant therapy? Thromb Haemost 102(5):892–899

    CAS  PubMed  Google Scholar 

  • Lavecchia A, Di Giovanni C (2013) Virtual screening strategies in drug discovery: a critical review. Curr Med Chem 20(23):2839–2860

    CAS  PubMed  Google Scholar 

  • Lee W, Ku S-K, Kim M-A, Bae J-S (2017) Anti-factor Xa activities of zingerone with anti-platelet aggregation activity. Food Chem Toxicol 105(Supplement C):186–193

    CAS  PubMed  Google Scholar 

  • Liakopoulou-Kyriakides M, Sinakos Z, Kyriakidis DA (1985) “Identification of alliin, a constituent of Allium cepa with an inhibitory effect on platelet aggregation”. Phytochemistry 24(3):600–601

    CAS  Google Scholar 

  • LigPrep SR (2009) “version 2.3”. Schrödinger, LLC, New York, NY

    Google Scholar 

  • Lionta E, Spyrou G, Vassilatis DK, Cournia Z (2014) Structure-based virtual screening for drug discovery: principles, applications and recent advances. Curr Top Med Chem 14(16):1923–1938

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lutz J, Jurk K, Schinzel H (2017) Direct oral anticoagulants in patients with chronic kidney disease: patient selection and special considerations. Int J Nephrol Renovasc Dis 10:135–143

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ma D-L, Chan DS-H, Leung C-H (2011) Molecular docking for virtual screening of natural product databases. Chem Sci 2(9):1656–1665

    CAS  Google Scholar 

  • Mahmood AL-ZR (2015) The Clinical and Hematological changes in Rabbits exposed to Melia azedarach fruits under experimental conditions. Int J Adv Sci Res 1(1):12

    Google Scholar 

  • Maignan S, Mikol V (2002) The use of 3D structural data in the design of specific factor Xa inhibitors. Curr Top Med Chem 1(2):161–174

    Google Scholar 

  • Mysinger MM, Carchia M, Irwin JJ, Shoichet BK (2012) Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Medicinal Chem 55(14):6582–6594

    CAS  Google Scholar 

  • Nair RM, Whittall A, Hughes SJ, Craig AD, Revell DK, Miller SM, Powell T, Auricht GC (2010) Variation in coumarin content of species grown in South Australia. New Zeal J Agr Res 53(3):201–213

    CAS  Google Scholar 

  • Nutescu EA, Shapiro NL, Ibrahim S, West P (2006) Warfarin and its interactions with foods, herbs and other dietary supplements. Expert Opin Drug Saf 5(3):433–451

    CAS  PubMed  Google Scholar 

  • Olsson MH, Sondergaard CR, Rostkowski M, Jensen JH (2011) PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions. J Chem Theory Comput 7(2):525–537

    CAS  PubMed  Google Scholar 

  • Patel NR, Patel DV, Murumkar PR, Yadav MR (2016) Contemporary developments in the discovery of selective factor Xa inhibitors: a review. Eur J Medicinal Chem 121:671–698

    CAS  Google Scholar 

  • Perzborn E, Roehrig S, Straub A, Kubitza D, Misselwitz F (2010) The discovery and development of rivaroxaban, an oral, direct factor Xa inhibitor. Nat Rev Drug Disco 10(1):61–75

    Google Scholar 

  • Perzborn E, Strassburger J, Wilmen A, Pohlmann J, Roehrig S, Schlemmer KH, Straub A (2005) In vitro and in vivo studies of the novel antithrombotic agent BAY 59-7939–an oral, direct Factor Xa inhibitor. J Thromb Haemost 3(3):514–521

    CAS  PubMed  Google Scholar 

  • Pinto DJP, Smallheer JM, Cheney DL, Knabb RM, Wexler RR (2010) Factor Xa Inhibitors: next-generation antithrombotic agents. J Medicinal Chem 53(17):6243–6274

    CAS  Google Scholar 

  • Pu Y, Liu H, Zhou Y, Peng J, Li Y, Li P, Li Y, Liu X, Zhang L (2017) In silico discovery of novel FXa inhibitors by pharmacophore modeling and molecular docking. Nat Products Bioprospecting 7(3):249–256

    CAS  Google Scholar 

  • Rueda M, Abagyan R (2016) Best practices in docking and activity prediction. https://doi.org/10.1101/039446

  • Schrödinger Suite (2012a) Protein preparation wizard; Epik version 2.3. Schrödinger, LLC, New York, NY

    Google Scholar 

  • Schrödinger Suite (2012b) Impact version 5.8. Schrödinger, LLC, New York, NY

    Google Scholar 

  • Schrödinger Suite (2012c) Prime version 3.1. Schrödinger, LLC, New York, NY

    Google Scholar 

  • Sebastien M, Vincent M (2001) The use of 3D structural data in the design of specific factor Xa inhibitors. Curr Top Medicinal Chem 1(2):161–174

    Google Scholar 

  • Shen J, Xu X, Cheng F, Liu H, Luo X, Chen K, Zhao W, Shen X, Jiang H (2003) Virtual screening on natural products for discovering active compounds and target information. Curr Med Chem 10(21):2327–2342

    CAS  PubMed  Google Scholar 

  • Skelley JW, Thomason AR, Nolen JC, Candidate P (2018) Betrixaban (Bevyxxa): a direct-acting oral anticoagulant factor Xa inhibitor. P T 43:85–120

    PubMed  PubMed Central  Google Scholar 

  • Sulimov VB, Gribkova IV, Kochugaeva MP, Katkova EV, Sulimov AV, Kutov DC, Shikhaliev KS, Medvedeva SM, Krysin MY, Sinauridze EI, Ataullakhanov FI (2015) Application of molecular modeling to development of new factor Xa inhibitors. BioMed Res Int 2015:15

    Google Scholar 

  • Suresh B, Vepuri SA, Naresh P, Divya D (2012) Pharmacophore modeling and docking based QSAR studies of aryl amidino isoxazoline derivatives to design potential FXa inhibitors. Am J Bioinforma Res 2(3):11–20

    Google Scholar 

  • Taha MO, Qandil AM, Zaki DD, AlDamen MA (2005) Ligand-based assessment of factor Xa binding site flexibility via elaborate pharmacophore exploration and genetic algorithm-based QSAR modeling. Eur J Med Chem 40(7):701–727

    CAS  PubMed  Google Scholar 

  • Tohti I, Tursun M, Umar A, Turdi S, Imin H, Moore N (2006) Aqueous extracts of Ocimum basilicum L. (sweet basil) decrease platelet aggregation induced by ADP and thrombin in vitro and rats arterio–venous shunt thrombosis in vivo. Thromb Res 118(6):733–739

    CAS  PubMed  Google Scholar 

  • Triballeau N, Acher F, Brabet I, Pin J-P, Bertrand H-O (2005) Virtual screening workflow development guided by the “Receiver Operating Characteristic” curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4. J Medicinal Chem 48(7):2534–2547

    CAS  Google Scholar 

  • Truchon JF, Bayly CI (2007) Evaluating virtual screening methods: good and bad metrics for the “early recognition” problem. J Chem Inf Model 47(2):488–508

    CAS  PubMed  Google Scholar 

  • Vaes LP, Chyka PA (2001) Interactions of warfarin with garlic, ginger, ginkgo, or ginseng: nature of the evidence. Ann Pharmacother 34(12):1478–1482

    Google Scholar 

  • van Wijk EM, Smit JLJ (1984) A chromogenic micro-assay for factor x-activity. Thrombosis Res 34(3):263–268

    Google Scholar 

  • Veerasamy R, Rajak H, Jain A, Sivadasan S, Varghese CP, Agrawal RK (2011) Validation of QSAR models-strategies and importance. Int J Drug Des Discov 2(3):511–519

    CAS  Google Scholar 

  • Venugopala KN, Rashmi V, Odhav B (2013) Review on natural coumarin lead compounds for their pharmacological activity. Biomed Res Int 2013:1–14

    Google Scholar 

  • Verma J, Khedkar VM, Coutinho EC (2009) 3D-QSAR in drug design–a review. Curr Top Med Chem 10(1):95–115

    Google Scholar 

  • WHO (2017) Cardiovascular diseases (CVDs). https://www.who.int/news-room/fact-sheets/detail/cardiovascular-diseases-(cvds). Accessed Mar 2018

  • Williamson EM, Driver S, Baxter K (2009) Stockley’s herbal medicines interactions: a guide to the interactions of herbal medicines, dietary supplements and nutraceuticals with conventional medicines, Pharmaceutical Press, London, United Kingdom

  • Yang X-G, Chen D, Xue Y (2012) Integration of ligand-based and structure-based approaches for virtual screening of factor Xa inhibitors. Quantum Simulations of Materials and Biological Systems, Springer. 141–154

  • Yazdanparast R (2009) Antiplatelet and antithrombotic activities of Artemisia dracunculus L. leaves extract. Pharmacol Online 1:217–228

    Google Scholar 

  • Young RJ, Campbell M, Borthwick AD, Brown D, Burns-Kurtis CL, Chan C, Convery MA, Crowe MC, Dayal S, Diallo H, Kelly HA, King NP, Kleanthous S, Mason AM, Mordaunt JE, Patel C, Pateman AJ, Senger S, Shah GP, Smith PW, Watson NS, Weston HE, Zhou P (2006) Structure- and property-based design of factor Xa inhibitors: pyrrolidin-2-ones with acyclic alanyl amides as P4 motifs. Bioorg Med Chem Lett 16(23):5953–5957

    CAS  PubMed  Google Scholar 

  • Zhang Y-X, Yang T-T, Xia L, Zhang W-F, Wang J-F, Wu Y-P (2017) Inhibitory effect of propolis on platelet aggregation in vitro. J Healthc Eng 2017:1–6

    CAS  Google Scholar 

  • Zhao Y, Jiang M, Zhou S, Wu S, Zhang X, Ma L, Zhang K, Gong P (2015) Design, synthesis and structure–activity relationship of oxazolidinone derivatives containing novel S4 ligand as FXa inhibitors. Eur J Medicinal Chem 96:369–380

    CAS  Google Scholar 

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Acknowledgements

Authors are grateful to Prof. Dr Michal Blazej Ponczek, Department of General Biochemistry, Faculty of Biology, and Environmental Protection, University of Lodz, Pomorska, Poland for the scientific explanation in performing the in vitro testing. Appreciation to Dr Rasha Nassra, Department of Medical Biochemistry, Faculty of Medicine, Alexandria University, Alexandria, Egypt for assistance in providing lab facilities to perform the in vitro testing and measurements. This work was supported in part by the University of Alexandria, Alexandria, Egypt.

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  1. Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt

    Reham S. Ibrahim, Rahma SR. Mahrous, Hoda M. Fathy, Abdallah A. Omar & Rasha M. Abu EL-Khair

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  1. Reham S. Ibrahim
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Ibrahim, R.S., Mahrous, R.S., Fathy, H.M. et al. Anticoagulant activity screening of an in-house database of natural compounds for discovering novel selective factor Xa inhibitors; a combined in silico and in vitro approach. Med Chem Res 29, 707–726 (2020). https://doi.org/10.1007/s00044-020-02516-5

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