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MOLLUSC Nerita Versicolor KINETIC AND PROTEOMIC IDENTIFICATION OF PROTEASE INHIBITORS IN MARINE INVERTEBRATES. CHARACTERIZATION OF A CARBOXYPEPTIDASE INHIBITOR ISOLATED FROM THE MOLLUSC Nerita versicolor Giovanny Covaleda Cortés October 2012 KINETIC AND PROTEOMIC IDENTIFICATION OF PROTEASE INHIBITORS IN MARINE INVERTEBRATES. CHARACTERIZATION OF A CARBOXYPEPTIDASE INHIBITOR ISOLATED FROM THE MOLLUSC Nerita versicolor Doctoral thesis presented by Giovanny Covaleda Cortés to obtain the PhD degree in “Structure and Function of Proteins” from the Universitat Autònoma de Barcelona This work has been performed in the Protein Engineering and Enzymology Laboratory, Institut de Biotecnologia i Biomedicina “Vicent Villar i Palasi”. Thesis work supervised by Profs. Francesc Xavier Avilés Puigvert and María de los Ángeles Chávez Planes Giovanny Covaleda Cortés Francesc Xavier Avilés Puigvert María de los Ángeles Chávez Planes Bellaterra, October 2012 Les 7 jours de la création « 1.1 Au commencement, Dieu créa les cieux et la terre. 1.2 La terre était informe et vide: il y avait des ténèbres à la surface de l'abîme, et l'esprit de Dieu se mouvait au-dessus des eaux. 1.3 ieu dit: Que la lumière soit! Et la lumière fut. 1.4 Dieu vit que la lumière était bonne; et Dieu sépara la lumière d'avec les ténèbres. 1.5 Dieu appela la lumière jour, et il appela les ténèbres nuit. Ainsi, il y eut un soir, et il y eut un matin: ce fut le premier jour. 1.6 D 1.7 Dieu dit: Qu'il y ait une étendue entre les eaux, et qu'elle sépare les eaux d'avec les eaux. Et Dieu fit l'étendue, et il sépara les eaux qui sont au-dessous de l'étendue d'avec les eaux qui sont au-dessus de l'étendue. Et cela fut ainsi. 1.8 Dieu appela l'étendue ciel. Ainsi, il y eut un soir, et il y eut un matin: ce fut le second jour. 1.9 Dieu dit: Que les eaux qui sont au-dessous du ciel se rassemblent en un seul lieu, et que le sec paraisse. Et cela fut ainsi. 1.10 Dieu appela le sec terre, et il appela l'amas des eaux mers. Dieu vit que cela était bon. 1.11 Puis Dieu dit: Que la terre produise de la verdure, de l'herbe portant de la semence, des arbres fruitiers donnant du fruit selon leur espèce et ayant en eux leur semence sur la terre. Et cela fut ainsi. 1.12 La terre produisit de la verdure, de l'herbe portant de la semence selon son espèce, et des arbres donnant du fruit et ayant en eux leur semence selon leur espèce. Dieu vit que cela était bon. 1.13 Ainsi, il y eut un soir, et il y eut un matin: ce fut le troisième jour. 1.14 Dieu dit: Qu'il y ait des luminaires dans l'étendue du ciel, pour séparer le jour d'avec la nuit; que ce soient des signes pour marquer les époques, les jours et les années; 1.15 et qu'ils servent de luminaires dans l'étendue du ciel, pour éclairer la terre. Et cela fut ainsi. 1.16 Dieu fit les deux grands luminaires, le plus grand luminaire pour présider au jour, et le plus petit luminaire pour présider à la nuit; il fit aussi les étoiles. 1.17 Dieu les plaça dans l'étendue du ciel, pour éclairer la terre, 1.18 pour présider au jour et à la nuit, et pour séparer la lumière d'avec les ténèbres. Dieu vit que cela était bon. 1.19 Ainsi, il y eut un soir, et il y eut un matin: ce fut le quatrième jour. 1.20 Dieu dit: Que les eaux produisent en abondance des animaux vivants, et que des oiseaux volent sur la terre vers l'étendue du ciel. 1.21 Dieu créa les grands poissons et tous les animaux vivants qui se meuvent, et que les eaux produisirent en abondance selon leur espèce; il créa aussi tout oiseau ailé selon son espèce. Dieu vit que cela était bon. 1.22 Dieu les bénit, en disant: Soyez féconds, multipliez, et remplissez les eaux des mers; et que les oiseaux multiplient sur la terre. 1.23 Ainsi, il y eut un soir, et il y eut un matin: ce fut le cinquième jour. 1.24 Dieu dit: Que la terre produise des animaux vivants selon leur espèce, du bétail, des reptiles et des animaux terrestres, selon leur espèce. Et cela fut ainsi. 1.25 Dieu fit les animaux de la terre selon leur espèce, le bétail selon son espèce, et tous les reptiles de la terre selon leur espèce. Dieu vit que cela était bon. 1.26 Puis Dieu dit: Faisons l'homme à notre image, selon notre ressemblance, et qu'il domine sur les poissons de la mer, sur les oiseaux du ciel, sur le bétail, sur toute la terre, et sur tous les reptiles qui rampent sur la terre. 1.27 Dieu créa l'homme à son image, il le créa à l'image de Dieu, il créa l'homme et la femme. 1.28 Dieu les bénit, et Dieu leur dit: Soyez féconds, multipliez, remplissez la terre, et l'assujettissez; et dominez sur les poissons de la mer, sur les oiseaux du ciel, et sur tout animal qui se meut sur la terre. 1.29 Et Dieu dit: Voici, je vous donne toute herbe portant de la semence et qui est à la surface de toute la terre, et tout arbre ayant en lui du fruit d'arbre et portant de la semence: ce sera votre nourriture. 1.30 Et à tout animal de la terre, à tout oiseau du ciel, et à tout ce qui se meut sur la terre, ayant en soi un souffle de vie, je donne toute herbe verte pour nourriture. Et cela fut ainsi. 1.31 Dieu vit tout ce qu'il avait fait et voici, cela était très bon. Ainsi, il y eut un soir, et il y eut un matin: ce fut le sixième jour. 2.1 Ainsi furent achevés les cieux et la terre, et toute leur armée. 2.2 Dieu acheva au septième jour son oeuvre, qu'il avait faite: et il se reposa au septième jour de toute son oeuvre, qu'il avait faite. 2.3 Dieu bénit le septième jour, et il le sanctifia, parce qu'en ce jour il se reposa de toute son oeuvre qu'il avait créée en la faisant. 2.4 Voici les origines des cieux et de la terre, quand ils furent créés. » Genèse, chapitre 1, versets 1-31 et chapitre 2, versets 1-2. Summary SUMMARY pproximately 2% of the genes in most organisms are proteases and proteolytic activity is involved in practically all biochemical and physiological processes in living organisms, A as well as in the generation/transmission of different pathologies. Consequently, proteolytic enzymes are of great interest for both biotechnological and pharmaceutical industry as potential drugs targets. Therefore, protease inhibitors have already become into very attractive and promising molecules as potential drugs and diagnostic tools. The present work describes the enzymatic kinetic identification of inhibitory activities against metallocarboxypeptidases A and B of the M14 family (MCPs, of the CPA and CPB type), pepsin, papain, trypsin and subtilisin in 30 Caribbean marine invertebrate extracts. The screening was performed on aqueous crude extracts from species belonging to the Phyla Annelida, Bryozoa, Chordata, Cnidaria, Echinodermata, Mollusca, and Porifera collected on the northern coast of Cuba. The qualitative results showed that fourteen extracts exhibited trypsin inhibitory activity, nine extracts displayed CPA, CPB, papain and subtilisin inhibitory activities, whilst only four extracts showed pepsin inhibitory activity. The most promising extracts showing inhibitory activities in terms of specific inhibitory activity (the highest values), dose-response relationships, IC 50 (the lowest values) and bioavailability of the species were N. versicolor , P. homomalla and S. helianthus for CPA; N. versicolor , C. muricatus and P. homomalla for CPB; B. granulifera , H. carunculata and D. listerianum for pepsin; P. homomalla , P. physalis and C. muricatus for papain; S. helianthus , N. versicolor , C. muricatus and N. peloronta for trypsin; and L. isodyctialis , I. badionotus and C. muricatus for subtilisin. This was complemented with the use of Intensity Fading (IF) MALDI-TOF MS, a medium- throughput proteomic-based strategy for the quick identification of those inhibitors in the marine extracts. It proved to be very useful to selectively identify, in some extracts, proteinaceous molecules (inhibitors) able to interact with the immobilized target enzymes, such as in N. versicolor against CPA and CPB, H. carunculata with pepsin, S. helianthus with papain, N. peloronta and S. helianthus with trypsin and L. isodyctialis for subtilisin. This work also describes the application of MALDI-TOF MS fragmentation and characterization approach using the resolved and most promising molecular species obtained in the elution fraction of IF MALDI- TOF MS. Two examples are described for this strategy: in the first one is the major peak resulting from the elution fraction of microaffinity interaction between H. carunculata crude extract and pepsin-NHS activated Sepharose™, which was fragmented by CID MALDI-TOF/TOF and subsequently analyzed by de novo sequencing. Another example was about ISD MALDI- TOF MS fragmentation and sequence analysis approach of the elution fraction of microaffinity interaction between S. helianthus crude extract and trypsin-glyoxal Sepharose ®. Both approaches show an excellent complementarity with the better established IF MALDI-TOF MS. Another important goal of this work was the purification and structural–functional characterization of NvCI, a proteinaceous carboxypeptidase inhibitor isolated from the marine snail N. versicolor . The combination of techniques such as automated Edman degradation and de novo sequencing by MALDI-TOF MS allowed the establishment of its primary structure.
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