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Journal Article
Brás, NF, Neves RPP, Lopes FAA, Correia MAS, Palma AS, Sousa SF, Ramos MJ.  2021.  Combined in silico and in vitro studies to identify novel antidiabetic flavonoids targeting glycogen phosphorylase, 2021. 108:104552. AbstractWebsite

Novel pharmacological strategies for the treatment of diabetic patients are now focusing on inhibiting glycogenolysis steps. In this regard, glycogen phosphorylase (GP) is a validated target for the discovery of innovative antihyperglycemic molecules. Natural products, and in particular flavonoids, have been reported as potent inhibitors of GP at the cellular level. Herein, free-energy calculations and microscale thermophoresis approaches were performed to get an in-depth assessment of the binding affinities and elucidate intermolecular interactions of several flavonoids at the inhibitor site of GP. To our knowledge, this is the first study indicating genistein, 8-prenylgenistein, apigenin, 8-prenylapigenin, 8-prenylnaringenin, galangin and valoneic acid dilactone as natural molecules with high inhibitory potency toward GP. We identified: i) the residues Phe285, Tyr613, Glu382 and/or Arg770 as the most relevant for the binding of the best flavonoids to the inhibitor site of GP, and ii) the 5-OH, 7-OH, 8-prenyl substitutions in ring A and the 4′-OH insertion in ring B to favor flavonoid binding at this site. Our results are invaluable to plan further structural modifications through organic synthesis approaches and develop more effective pharmaceuticals for Type 2 Diabetes treatment, and serve as the starting point for the exploration of food products for therapeutic usage, as well as for the development of novel bio-functional food and dietary supplements/herbal medicines.

Seixas, JD, Santos MFA, Mukhopadhyay A, Coelho AC, Reis PM, Veiros LF, Marques AR, Penacho N, Goncalves AML, Romao MJ, Bernardes GJL, Santos-Silva T, Romao CC.  2015.  A contribution to the rational design of Ru(CO)(3)Cl2L complexes for in vivo delivery of CO. Dalton Transactions. 44:5058-5075., Number 11 AbstractWebsite

A few ruthenium based metal carbonyl complexes, e.g. CORM-2 and CORM-3, have therapeutic activity attributed to their ability to deliver CO to biological targets. In this work, a series of related complexes with the formula [Ru(CO)(3)Cl2L] (L = DMSO (3), L-H3CSO(CH2)(2)CH(NH2)CO2H) (6a); D,L-H3CSO(CH2)(2)CH-(NH2)CO2H (6b); 3-NC5H4(CH2)(2)SO3.Na (7); 4-NC5H4(CH2)(2)SO3Na (8); PTA (9); DAPTA (10); H3CS-(CH2)(2)CH(OH) CO2H (11); CNCMe2CO2Me (12); CNCMeEtCO2Me (13); CN(c-C3H4)CO2Et) (14)) were designed, synthesized and studied. The effects of L on their stability, CO release profile, cytotoxicity and anti-inflammatory properties are described. The stability in aqueous solution depends on the nature of L as shown using HPLC and LC-MS studies. The isocyanide derivatives are the least stable complexes, and the S-bound methionine oxide derivative is the more stable one. The complexes do not release CO gas to the headspace, but release CO2 instead. X-ray diffraction of crystals of the model protein Hen Egg White Lysozyme soaked with 6b (4UWN) and 8 (4UWV) shows the addition of Ru-II(CO)(H2O)(4) at the His15 binding site. Soakings with 7 (4UWU) produced the metallacarboxylate [Ru(COOH)(CO)(H2O)(3)](+) bound to the His15 site. The aqueous chemistry of these complexes is governed by the water-gas shift reaction initiated with the nucleophilic attack of HO- on coordinated CO. DFT calculations show this addition to be essentially barrierless. The complexes have low cytotoxicity and low hemolytic indices. Following i.v. administration of CORM-3, the in vivo bio-distribution of CO differs from that obtained with CO inhalation or with heme oxygenase stimulation. A mechanism for CO transport and delivery from these complexes is proposed.

Santos-Silva, T, Mukhopadhyay A, Seixas JD, Bernardes GJL, Romao CC, Romao MJ.  2011.  CORM-3 Reactivity toward Proteins: The Crystal Structure of a Ru(II) Dicarbonyl-Lysozyme Complex. Journal of the American Chemical Society. 133:1192-1195., Number 5 AbstractWebsite
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Thapper, A, Boer DR, Brondino CD, Moura JJG, Romao MJ.  2007.  Correlating EPR and X-ray structural analysis of arsenite-inhibited forms of aldehyde oxidoreductase. Journal of Biological Inorganic Chemistry. 12:353-366., Number 3 AbstractWebsite
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Mota, C, Coelho C, Leimkühler S, Garattini E, Terao M, Santos-Silva T, Romão MJ.  2018.  Critical overview on the structure and metabolism of human aldehyde oxidase and its role in pharmacokinetics, 2018. 368:35-59. AbstractWebsite

Aldehyde oxidases are molybdenum and flavin dependent enzymes characterized by a very wide substrate specificity and performing diverse reactions that include oxidations (e.g., aldehydes and aza-heterocycles), hydrolysis of amide bonds, and reductions (e.g., nitro, S-oxides and N-oxides). Oxidation reactions and amide hydrolysis occur at the molybdenum site while the reductions are proposed to occur at the flavin site. AOX activity affects the metabolism of different drugs and xenobiotics, some of which designed to resist other liver metabolizing enzymes (e.g., cytochrome P450 monooxygenase isoenzymes), raising its importance in drug development. This work consists of a comprehensive overview on aldehyde oxidases, concerning the genetic evolution of AOX, its diversity among the human population, the crystal structures available, the known catalytic reactions and the consequences in pre-clinical pharmacokinetic and pharmacodynamic studies. Analysis of the different animal models generally used for pre-clinical trials and comparison between the human (hAOX1), mouse homologs as well as the related xanthine oxidase (XOR) are extensively considered. The data reviewed also include a systematic analysis of representative classes of molecules that are hAOX1 substrates as well as of typical and well characterized hAOX1 inhibitors. The considerations made on the basis of a structural and functional analysis are correlated with reported kinetic and metabolic data for typical classes of drugs, searching for potential structural determinants that may dictate substrate and/or inhibitor specificities.

Bursakov, SA, Brondino C, Dias JM, Carneiro C, Caldeira J, Duarte RO, Romao MJ, Moura I, Moura JJG.  1999.  Cross immunological reactions and spectroscopy study within nitrate reductase and other mononuclear Mo containing enzymes of the sulfate reducing bacteria. Journal of Inorganic Biochemistry. 74:86-86., Number 1-4 AbstractWebsite
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Romao, MJ, Hubert R.  1997.  Crystal structure and mechanism of action of the xanthine oxidase-related aldehyde oxidoreductase from Desulfovibrio gigas. Biochemical Society Transactions. 25:755-757., Number 3 AbstractWebsite
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Carvalho, AL, Sanz L, Barettino D, Romero A, Calvete JJ, Romao MJ.  2002.  Crystal structure of a prostate kallikrein isolated from stallion seminal plasma: A homologue of human PSA. Journal of Molecular Biology. 322:325-337., Number 2 AbstractWebsite
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Romao, MJ, Kolln I, Dias JM, Carvalho AL, Romero A, Varela PF, Sanz L, Topfer-Petersen E, Calvete JJ.  1997.  Crystal structure of acidic seminal fluid protein (aSFP) at 1.9 angstrom resolution: a bovine polypeptide of the spermadhesin family. Journal of Molecular Biology. 274:650-660., Number 4 AbstractWebsite
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Coelho, C, Gonzalez PJ, Moura JJG, Moura I, Trincao J, Romao MJ.  2011.  The Crystal Structure of Cupriavidus necator Nitrate Reductase in Oxidized and Partially Reduced States. Journal of Molecular Biology. 408:932-948., Number 5 AbstractWebsite
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Archer, M, Banci L, Dikaya E, Romao MJ.  1997.  Crystal structure of cytochrome c' from Rhodocyclus gelatinosus and comparison with other cytochromes c'. Journal of Biological Inorganic Chemistry. 2:611-622., Number 5 AbstractWebsite
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Romero, A, Caldeira J, Legall J, Moura I, Moura JJG, Romao MJ.  1996.  Crystal structure of flavodoxin from Desulfovibrio desulfuricans ATCC 27774 in two oxidation states. European Journal of Biochemistry. 239:190-196., Number 1 AbstractWebsite
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Santos-Silva, T, Dias JM, Dolla A, Durand M-C, Goncalves LL, Lampreia J, Moura I, Romao MJ.  2007.  Crystal structure of the 16 heme cytochrome from Desulfovibrio gigas: A glycosylated protein in a sulphate-reducing bacterium. Journal of Molecular Biology. 370:659-673., Number 4 AbstractWebsite
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Dias, JM, Than ME, Humm A, Huber R, Bourenkov GP, Bartunik HD, Bursakov S, Calvete J, Caldeira J, Carneiro C, Moura JJG, Moura I, Romao MJ.  1999.  Crystal structure of the first dissimilatory nitrate reductase at 1.9 angstrom solved by MAD methods. Structure with Folding & Design. 7:65-79., Number 1 AbstractWebsite
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Gomes, AS, Trovão F, Andrade Pinheiro B, Freire F, Gomes S, Oliveira C, Domingues L, Romão MJ, Saraiva L, Carvalho AL.  2018.  The Crystal Structure of the R280K Mutant of Human p53 Explains the Loss of DNA Binding. International Journal of Molecular Sciences. 19, Number 4}, ARTICLE NUMBER = {1184 AbstractWebsite

The p53 tumor suppressor is widely found to be mutated in human cancer. This protein is regarded as a molecular hub regulating different cell responses, namely cell death. Compelling data have demonstrated that the impairment of p53 activity correlates with tumor development and maintenance. For these reasons, the reactivation of p53 function is regarded as a promising strategy to halt cancer. In the present work, the recombinant mutant p53R280K DNA binding domain (DBD) was produced for the first time, and its crystal structure was determined in the absence of DNA to a resolution of 2.0 Å. The solved structure contains four molecules in the asymmetric unit, four zinc(II) ions, and 336 water molecules. The structure was compared with the wild-type p53 DBD structure, isolated and in complex with DNA. These comparisons contributed to a deeper understanding of the mutant p53R280K structure, as well as the loss of DNA binding related to halted transcriptional activity. The structural information derived may also contribute to the rational design of mutant p53 reactivating molecules with potential application in cancer treatment.

Mukhopadhyay, A, Kladova AV, Bursakov SA, Gavel YO, Calvete JJ, Shnyrov VL, Moura I, Moura JJG, Romao MJ, Trincao J.  2011.  Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria. Journal of Biological Inorganic Chemistry. 16:51-61., Number 1 AbstractWebsite
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Romero, A, Romao MJ, Varela PF, Kolln I, Dias JM, Carvalho AL, Sanz L, TopferPetersen E, Calvete JJ.  1997.  The crystal structures of two spermadhesins reveal the CUB domain fold. Nature Structural Biology. 4:783-788., Number 10 AbstractWebsite
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Romao, MJ, Turk D, GomisRuth FX, Huber R, Schumacher G, Mollering H, Russmann L.  1992.  CRYSTAL-STRUCTURE ANALYSIS, REFINEMENT AND ENZYMATIC-REACTION MECHANISM OF N-CARBAMOYLSARCOSINE AMIDOHYDROLASE FROM ARTHROBACTER SP AT 2.0-ANGSTROM RESOLUTION. Journal of Molecular Biology. 226:1111-1130., Number 4 AbstractWebsite
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Archer, M, Huber R, Tavares P, Moura I, Moura JJG, Carrondo MA, Sieker LC, Legall J, Romao MJ.  1995.  CRYSTAL-STRUCTURE OF DESULFOREDOXIN FROM DESULFOVIBRIO-GIGAS DETERMINED AT 1.8 ANGSTROM RESOLUTION - A NOVEL NONHEME IRON PROTEIN-STRUCTURE. Journal of Molecular Biology. 251:690-702., Number 5 AbstractWebsite
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Romao, MJ, Archer M, Moura I, Moura JJG, Legall J, Engh R, Schneider M, Hof P, Huber R.  1995.  CRYSTAL-STRUCTURE OF THE XANTHINE OXIDASE-RELATED ALDEHYDE OXIDOREDUCTASE FROM D-GIGAS. Science. 270:1170-1176., Number 5239 AbstractWebsite
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Najmudin, S, Bonifacio C, Duarte AG, Pualeta SR, Moura I, Moura JJG, Romao MJ.  2009.  Crystallization and crystallographic analysis of the apo form of the orange protein (ORP) from Desulfovibrio gigas. Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 65:730-732. AbstractWebsite
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Najmudin, S, Bonifacio C, Duarte AG, Pauleta SR, Moura I, Moura JJG, Romao MJ.  2009.  Crystallization and crystallographic analysis of the apo form of the orange protein (ORP) from Desulfovibrio gigas. (vol F65, pg 730, 2009). Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 65:856-856. AbstractWebsite
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Dias, JM, Cunha CA, Teixeira S, Almeida G, Costa C, Lampreia J, Moura JJG, Moura I, Romao MJ.  2000.  Crystallization and preliminary X-ray analysis of a membrane-bound nitrite reductase from Desulfovibrio desulfuricans ATCC 27774. Acta Crystallographica Section D-Biological Crystallography. 56:215-217. AbstractWebsite
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Dias, JM, Bursakov S, Carneiro C, Moura JJG, Moura I, Romao MJ.  1999.  Crystallization and preliminary X-ray analysis of a nitrate reductase from Desulfovibrio desulfuricans ATCC 27774. Acta Crystallographica Section D-Biological Crystallography. 55:877-879. AbstractWebsite
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Santos-Silva, T, Diasa JM, Bourenkov G, Bartunik H, Moura I, Romao MJ.  2004.  Crystallization and preliminary X-ray diffraction analysis of the 16-haem cytochrome of Desulfovibrio gigas. Acta Crystallographica Section D-Biological Crystallography. 60:968-970. AbstractWebsite
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