{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T18:01:15Z","timestamp":1775930475594,"version":"3.50.1"},"reference-count":37,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2021,6,28]],"date-time":"2021-06-28T00:00:00Z","timestamp":1624838400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Carlos Chagas Filho Foundation for Research Support of the State of Rio de Janeiro","award":["FAPERJ #170.009-2008"],"award-info":[{"award-number":["FAPERJ #170.009-2008"]}]},{"name":"Brazilian Council for Scientific Research (CNPq)","award":["#467.488-2014-2"],"award-info":[{"award-number":["#467.488-2014-2"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>Introduction: Snakebite envenomation is considered a neglected tropical disease, and SVTLEs critical elements are involved in serious coagulopathies that occur on envenoming. Although some enzymes of this group have been structurally investigated, it is essential to characterize other proteins to better understand their unique properties such as the Lachesis muta rhombeata 47 kDa (Lmr-47) venom serine protease. Methods: The structure of Lmr-47 was studied in solution, using SAXS, DLS, CD, and in silico by homology modeling. Molecular docking experiments simulated 21 competitive inhibitors. Results: At pH 8.0, Lmr-47 has an Rg of 34.5 \u00b1 0.6 \u00c5, Dmax of 130 \u00c5, and SR of 50 \u00c5, according to DLS data. Kratky plot analysis indicates a rigid shape at pH 8.0. Conversely, the pH variation does not change the center of mass\u2019s intrinsic fluorescence, possibly indicating the absence of fluorescent amino acids in the regions affected by pH variation. CD experiments show a substantially random coiled secondary structure not affected by pH. The low-resolution model of Lmr-47 presented a prolate elongated shape at pH 8.0. Using the 3D structure obtained by molecular modeling, docking experiments identified five good and three suitable competitive inhibitors. Conclusion: Together, our work provided insights into the structure of the Lmr-47 and identified inhibitors that may enhance our understanding of thrombin-like family proteins.<\/jats:p>","DOI":"10.3390\/molecules26133930","type":"journal-article","created":{"date-parts":[[2021,6,28]],"date-time":"2021-06-28T02:05:37Z","timestamp":1624845937000},"page":"3930","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Small Angle X-ray Scattering, Molecular Modeling, and Chemometric Studies from a Thrombin-Like (Lmr-47) Enzyme of Lachesis m. rhombeata Venom"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2172-656X","authenticated-orcid":false,"given":"Salvatore Giovanni","family":"De-Simone","sequence":"first","affiliation":[{"name":"FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil"},{"name":"Department of Cellular and Molecular Biology, Biology Institute, Federal Fluminense University, Niter\u00f3i 24020-141, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guilherme Curty","family":"Lechuga","sequence":"additional","affiliation":[{"name":"FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paloma","family":"Napole\u00e3o-P\u00eago","sequence":"additional","affiliation":[{"name":"FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Larissa Rodrigues","family":"Gomes","sequence":"additional","affiliation":[{"name":"FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9824-0672","authenticated-orcid":false,"suffix":"Jr.","given":"David William","family":"Provance","sequence":"additional","affiliation":[{"name":"FIOCRUZ, Center of Technological Development in Health (CDTS), National Institute of Science and Technology for Innovation on Neglected Diseases Population (INCT-IDPN), Rio de Janeiro 21040-900, Brazil"},{"name":"Interdisciplinary Medical Research Laboratory, Oswaldo Cruz Institute\/FIOCRUZ, Rio de Janeiro 21040-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vin\u00edcius Dias","family":"Nirello","sequence":"additional","affiliation":[{"name":"Faculty of Pharmacy, Federal of Rio de Janeiro University, Rio de Janeiro 21949-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2603-1740","authenticated-orcid":false,"given":"Ana Carolina Renn\u00f3","family":"Sodero","sequence":"additional","affiliation":[{"name":"Faculty of Pharmacy, Federal of Rio de Janeiro University, Rio de Janeiro 21949-900, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3819-3069","authenticated-orcid":false,"given":"Herbert Leonel de Mattos","family":"Guedes","sequence":"additional","affiliation":[{"name":"Interdisciplinary Medical Research Laboratory, Oswaldo Cruz Institute\/FIOCRUZ, Rio de Janeiro 21040-900, Brazil"},{"name":"Laboratory of Immunopharmacology, Federal of Rio de Janeiro University, Duque de Caxias 25245-390, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,6,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1874","DOI":"10.2174\/0929867324666170605091546","article-title":"Snake venom: From deadly toxins to life-saving therapeutics","volume":"24","author":"Waheed","year":"2017","journal-title":"Curr. Med. Chem."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1791","DOI":"10.1111\/j.1538-7836.2005.01358.x","article-title":"Snake venoms, and hemostasis","volume":"3","author":"Lu","year":"2005","journal-title":"Thromb. Haemost."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1016\/j.toxicon.2005.02.020","article-title":"Snake venom serine proteinases: Sequence homology vs. substrate specificity, a paradox to be solved","volume":"45","author":"Serrano","year":"2005","journal-title":"Toxicon"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1006\/jmbi.1996.0264","article-title":"Conservation and variability in the structures of serine proteinases of the chymotrypsin family","volume":"258","author":"Lesk","year":"1996","journal-title":"J. Mol. Biol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"788","DOI":"10.1016\/j.ijbiomac.2018.03.164","article-title":"Thrombin-like enzymes from snake venom: Structural characterization and mechanism of action","volume":"114","author":"Ullah","year":"2018","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/S0167-4838(01)00177-7","article-title":"Structural features of a snake venom thrombin-like enzyme: Thrombin and trypsin on a single catalytic platform?","volume":"1547","author":"Castro","year":"2001","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1107\/S1744309111022548","article-title":"Structure of saxthrombin, a thrombin-like enzyme from Gloydius saxatilis","volume":"67","author":"Huang","year":"2011","journal-title":"Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1007\/s00204-012-0957-5","article-title":"Crystal structure and activating effect on RyRs of AhV TL-I, a glycosylated thrombin-like enzyme from Agkistrodon halys snake venom","volume":"87","author":"Zeng","year":"2013","journal-title":"Arch. Toxicol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1002\/pro.2189","article-title":"Crystal structure of Jararacussin-I: The highly negatively charged catalytic interface contributes to macromolecular selectivity in snake venom thrombin-like enzymes","volume":"22","author":"Ullah","year":"2013","journal-title":"Protein Sci."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.toxicon.2007.02.018","article-title":"BJ-48, a novel thrombin-like enzyme from the Bothrops jararacussu venom with high selectivity for Arg over Lys in P1, Role of N-glycosylation","volume":"50","author":"Silva","year":"2007","journal-title":"Toxicon"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.bpc.2007.11.002","article-title":"Structural characterization and low-resolution model of BJ-48, a thrombin-like enzyme from Bothrops jararacussu venom","volume":"132","author":"Guedes","year":"2008","journal-title":"Biophys. Chem."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1549","DOI":"10.1016\/S0041-0101(97)00003-2","article-title":"Thrombin-like enzyme from Lachesis muta muta venom: Isolation and topographical analysis of its active site structure by means of the binding of amidines and guanidines as competitive inhibitors","volume":"35","author":"Monteiro","year":"1997","journal-title":"Toxicon"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1016\/0041-0101(95)00159-X","article-title":"Purification and partial characterization of a thrombin-like\/gyroxin enzyme from bushmaster (Lachesis muta rhombeata) venom","volume":"34","author":"Aguiar","year":"1996","journal-title":"Toxicon"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"3580","DOI":"10.1111\/j.0014-2956.2004.04295.x","article-title":"New insights into conformational and functional stability of human alpha-thrombin probed by high hydrostatic pressure","volume":"271","author":"Lima","year":"2004","journal-title":"Eur. J. Biochem."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1107\/S0021889803000268","article-title":"Uniqueness of ab initio shape determination in small-angle scattering","volume":"36","author":"Volkov","year":"2003","journal-title":"J. Appl. Crystallogr."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1110\/ps.4210102","article-title":"Natively unfolded proteins: A point where biology waits for physics","volume":"11","author":"Uversky","year":"2002","journal-title":"Protein Sci."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1107\/S002188989100081X","article-title":"GNOM- a program package for small-angle scattering data processing","volume":"24","author":"Semenyuk","year":"1991","journal-title":"J. Appl. Crystallogr."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2571","DOI":"10.1016\/j.bmc.2004.03.024","article-title":"S1 subsite in snake venom thrombin-like enzymes: Can S1 subsite lipophilicity be used to sort binding affinities of trypsin-like enzymes to small-molecule inhibitors?","volume":"12","author":"Silva","year":"2004","journal-title":"Bioorg. Med. Chem."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1007\/s11418-018-1202-1","article-title":"Anti-inflammatory and anti-angiogenic activities in vitro of eight diterpenes from Daphne genkwa based on hierarchical cluster and principal component analysis","volume":"72","author":"Wang","year":"2018","journal-title":"J. Nat. Med."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.tifs.2017.12.006","article-title":"Use of principal component analysis (PCA) and hierarchical cluster analysis (HCA) for multivariate association between bioactive compounds and functional properties in foods: A critical perspective","volume":"72","author":"Granato","year":"2018","journal-title":"Trends Food Sci. Technol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/S0167-4838(99)00284-8","article-title":"What can the structures of enzyme-inhibitor complexes tell us about the structures of enzyme-substrate complexes?","volume":"1477","author":"Laskowski","year":"2000","journal-title":"Biochim. Biophys. Acta."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"3467","DOI":"10.1002\/j.1460-2075.1989.tb08511.x","article-title":"The refined 1.9 A crystal structure of human alpha-thrombin: Interaction with D-Phe-Pro-Arg chloromethyl ketone and significance of the Tyr-Pro-Pro-Trp insertion segment","volume":"5","author":"Bode","year":"1989","journal-title":"EMBO J."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1002\/bip.20070","article-title":"Metal-ion-and pH-induced conformational changes autolysin D from Agkistrodon acutus venom probed by fluorescent spectroscopy","volume":"74","author":"Xu","year":"2004","journal-title":"Biopolymers"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1055\/s-2006-939550","article-title":"An overview of the structure and function of thrombin","volume":"32","author":"Earl","year":"2006","journal-title":"Semin. Thromb. Hemost."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1107\/S0021889897001829","article-title":"The small-angle X-ray scattering beamline of the Brazilian Synchrotron Light Laboratory","volume":"30","author":"Kellermann","year":"1997","journal-title":"J. Appl. Crystallogr."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jchromb.2005.04.018","article-title":"Biochemical and molecular modeling analysis of the ability of two p-amino benzamidine-based sorbents to selectively purify serine proteases (fibrinogenases) from snake venoms","volume":"822","author":"Antunes","year":"2005","journal-title":"J. Chromatogr. B Analyt. Technol. Biomed. Life Sci."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1038\/227680a0","article-title":"Cleavage of structural proteins during the assembly of the head of bacteriophage T","volume":"227","author":"Laemmli","year":"1970","journal-title":"Nature"},{"key":"ref_28","unstructured":"Oliveira, C.L.P., dos Santos, D.R., Kellermann, G., Plivelic, T., and Torriani, I.L. (1997). Technical Note, LNLS."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2946","DOI":"10.1016\/S0006-3495(01)76260-1","article-title":"Determination of the domain structure of proteins from X-ray solution scattering","volume":"80","author":"Svergun","year":"2001","journal-title":"Biophys. J."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1016\/S0006-3495(00)76630-6","article-title":"Calculation of hydrodynamic properties of globular proteins from their atomic-level structure","volume":"78","author":"Huertas","year":"2000","journal-title":"Biophys. J."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1006\/jmbi.1993.1626","article-title":"Comparative protein modeling by satisfaction of spatial restraints","volume":"234","author":"Sali","year":"1993","journal-title":"J. Mol. Biol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","article-title":"PROCHECK\u2014A program to check the stereochemical quality of protein structures","volume":"26","author":"Laskowski","year":"1993","journal-title":"J. App. Cryst."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1126\/science.1853201","article-title":"A method to identify protein sequences that fold into a known three-dimensional structure","volume":"253","author":"Bowie","year":"1991","journal-title":"Science"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/356083a0","article-title":"Assessment of protein models with three-dimensional profiles","volume":"356","author":"Bowie","year":"1992","journal-title":"Nature"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","article-title":"Auto Dock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading","volume":"31","author":"Trott","year":"2010","journal-title":"J. Comp. Chem."},{"key":"ref_36","first-page":"1","article-title":"Open Drug Discovery Toolkit (ODDT): A new open-source player in the drug discovery field","volume":"7","author":"Zielenkiewicz","year":"2015","journal-title":"J. Cheminform."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1093\/bioinformatics\/btq112","article-title":"A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking","volume":"26","author":"Ballester","year":"2010","journal-title":"Bioinformatics"}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/26\/13\/3930\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T06:25:27Z","timestamp":1760163927000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/26\/13\/3930"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,6,28]]},"references-count":37,"journal-issue":{"issue":"13","published-online":{"date-parts":[[2021,7]]}},"alternative-id":["molecules26133930"],"URL":"https:\/\/doi.org\/10.3390\/molecules26133930","relation":{},"ISSN":["1420-3049"],"issn-type":[{"value":"1420-3049","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,6,28]]}}}