@article{Albesa-Jové2015, abstract = {Rv2466c is a key oxidoreductase that mediates the reductive activation of TP053, a thienopyrimidine derivative that kills replicating and non-replicating Mycobacterium tuberculosis, but whose mode of action remains enigmatic. Rv2466c is a homodimer in which each subunit displays a modular architecture comprising a canonical thioredoxin-fold with a Cys$^{19}$-Pro$^{20}$-Trp$^{21}$-Cys$^{22}$ motif, and an insertion consisting of a four a-helical bundle and a short b-helical hairpin. Strong evidence is provided for dramatic conformational changes during the Rv2466c redox cycle, which are essential for TP053 activity. Strikingly, a new crystal structure of the reduced form of Rv2466c revealed the binding of a C-terminal extension in a-helical conformation to a pocket next to the active site cysteine pair at the interface between the thioredoxin domain and the helical insertion domain. The ab initio low-resolution envelopes obtained from small angle x-ray scattering showed that the fully reduced form of Rv2466c adopts a “closed” compact con- formation in solution, similar to that observed in the crystal structure. In contrast, the oxidized form of Rv2466c displays an “open” conformation, where tertiary structural changes in the a-helical subdomain suffice to account for the observed conformational transitions. Altogether our structural, biochemical, and biophysical data strongly support a model in which the formation of the catalytic disulfide bond upon TP053 reduction triggers local structural changes that open the substrate binding site of Rv2466c allowing the release of the activated, reduced form of TP053. Our studies suggest that similar structural changes might have a functional role in other members of the thioredoxin-fold superfamily.}, author = {Albesa-Jové, David and Comino, Natalia and Tersa, Montse and Mohorko, Elisabeth and Urresti, Saioa and Dainese, Elisa and Chiarelli, Laurent R. and Pasca, Maria Rosalia and Manganelli, Riccardo and Makarov, Vadim and Riccardi, Giovanna and Svergun, Dmitri I. and Glockshuber, Rudi and Guerin, Marcelo E.}, doi = {10.1074/jbc.m115.677039}, journal = {Journal of Biological Chemistry}, month = {nov}, pages = {31077-31089}, title = {The Redox State Regulates the Conformation of Rv2466c to Activate the Antitubercular Prodrug TP053}, url = {http://www.jbc.org/content/290/52/31077.full.pdf}, volume = {290}, year = {2015} } @article{Buroni2018, author = {Buroni, Silvia and Scoffone, Viola C. and Fumagalli, Marco and Makarov, Vadim and Cagnone, Maddalena and Trespidi, Gabriele and De Rossi, Edda and Rossi, Edda De and Forneris, Federico and Riccardi, Giovanna and Chiarelli, Laurent R.}, doi = {10.3389/fphar.2018.00836}, journal = {Frontiers in Pharmacology}, month = {jul}, title = {Investigating the Mechanism of Action of Diketopiperazines Inhibitors of the Burkholderia cenocepacia Quorum Sensing Synthase CepI: A Site-Directed Mutagenesis Study}, url = {https://doi.org/10.3389/fphar.2018.00836}, volume = {9}, year = {2018} } @article{D’Amato2023, abstract = {Human neutrophil elastase (HNE) is involved in SARS-CoV-2 virulence and plays a pivotal role in lung infection of patients infected by COVID-19. In healthy individuals, HNE activity is balanced by α1-antitrypsin (AAT). This is a 52 kDa glycoprotein, mainly produced and secreted by hepatocytes, that specifically inhibits HNE by blocking its activity through the formation of a stable complex (HNE–AAT) in which the two proteins are covalently bound. The lack of this complex, together with the detection of HNE activity in BALf/plasma samples of COVID-19 patients, leads us to hypothesize that potential functional deficiencies should necessarily be attributed to possible structural modifications of AAT. These could greatly diminish its ability to inhibit neutrophil elastase, thus reducing lung protection. The aim of this work was to explore the oxidation state of AAT in BALf/plasma samples from these patients so as to understand whether the deficient inhibitory activity of AAT was somehow related to possible conformational changes caused by the presence of abnormally oxidized residues.}, author = {D’Amato, Maura and Campagnoli, Monica and Iadarola, Paolo and Bignami, Paola Margherita and Fumagalli, Marco and Chiarelli, Laurent Roberto and Stelitano, Giovanni and Meloni, Federica and Linciano, Pasquale and Collina, Simona and Pietrocola, Giampiero and Vertui, Valentina and Aliberti, Anna and Fossali, Tommaso and Viglio, Simona}, doi = {10.3390/ijms241713533}, journal = {International Journal of Molecular Sciences}, month = {aug}, pages = {13533}, title = {Could the Oxidation of α1-Antitrypsin Prevent the Binding of Human Neutrophil Elastase in COVID-19 Patients?}, url = {https://doi.org/10.3390/ijms241713533}, volume = {24}, year = {2023} } @article{Ezquerra-Aznárez2022, abstract = {Avermectins are macrocyclic lactones with anthelmintic activity. Recently, they were found to be effective against Mycobacterium tuberculosis, which accounts for one third of the worldwide deaths from antimicrobial resistance. However, their anti-mycobacterial mode of action remains to be elucidated. The activity of selamectin was determined against a panel of M. tuberculosis mutants. Two strains carrying mutations in DprE1, the decaprenylphosphoryl-β-D-ribose oxidase involved in the synthesis of mycobacterial arabinogalactan, were more susceptible to selamectin. Biochemical assays against the Mycobacterium smegmatis DprE1 protein confirmed this finding, and docking studies predicted a binding site in a loop that included Leu275. Sequence alignment revealed variants in this position among mycobacterial species, with the size and hydrophobicity of the residue correlating with their MIC values; M. smegmatis DprE1 variants carrying these point mutations validated the docking predictions. However, the correlation was not confirmed when M. smegmatis mutant strains were constructed and MIC phenotypic assays performed. Likewise, metabolic labeling of selamectin-treated M. smegmatis and M. tuberculosis cells with 14C-labeled acetate did not reveal the expected lipid profile associated with DprE1 inhibition. Together, our results confirm the in vitro interactions of selamectin and DprE1 but suggest that selamectin could be a multi-target anti-mycobacterial compound.}, author = {Ezquerra-Aznárez, José Manuel and Degiacomi, Giulia and Gašparovič, Henrich and Stelitano, Giovanni and Sammartino, Josè Camilla and Korduláková, Jana and Governa, Paolo and Manetti, Fabrizio and Pasca, Maria Rosalia and Chiarelli, Laurent Roberto and Ramón-García, Santiago}, doi = {10.3390/ijms23020771}, journal = {International Journal of Molecular Sciences}, month = {jan}, pages = {771}, title = {The Veterinary Anti-Parasitic Selamectin Is a Novel Inhibitor of the Mycobacterium tuberculosis DprE1 Enzyme}, url = {https://doi.org/10.3390/ijms23020771}, volume = {23}, year = {2022} } @article{Hartkoorn2014, abstract = {ABSTRACT On using the streptomycin-starved 18b strain as a model for nonreplicating Mycobacterium tuberculosis , we identified a 5-nitrothiophene compound as highly active but not cytotoxic. Mutants resistant to 5-nitrothiophenes were found be cross-resistant to the nitroimidazole PA-824 and unable to produce the F 420 cofactor. Furthermore, 5-nitrothiophenes were shown to be activated by the F 420 -dependent nitroreductase Ddn and to release nitric oxide, a mechanism of action identical to that described for nitroimidazoles. }, author = {Hartkoorn, Ruben C. and Ryabova, Olga B. and Chiarelli, Laurent R. and Riccardi, Giovanna and Makarov, Vadim and Cole, Stewart T.}, doi = {10.1128/aac.02693-13}, journal = {Antimicrobial Agents and Chemotherapy}, month = {feb}, pages = {2944-2947}, title = {Mechanism of Action of 5-Nitrothiophenes against Mycobacterium tuberculosis}, url = {http://aac.asm.org/content/58/5/2944.full.pdf}, volume = {58}, year = {2014} } @article{Maggi2015, abstract = {Bacterial L-asparaginases have been used as anti-cancer drugs for over 4 decades though presenting, along with their therapeutic efficacy, several side effects due to their bacterial origin and, seemingly, to their secondary glutaminase activity. Helicobacter pylori type II L-asparaginase possesses interesting features, among which a reduced catalytic efficiency for L-GLN, compared to the drugs presently used in therapy. In the present study, we describe some enzyme variants with catalytic and in vitro cytotoxic activities different from the wild type enzyme. Particularly, replacements on catalytic threonines (T16D and T95E) deplete the enzyme of both its catalytic activities, once more underlining the essential role of such residues. One serendipitous mutant, M121C/T169M, had a preserved efficiency vs L-asparagine but was completely unable to carry out L-glutamine hydrolysis. Interestingly, this variant did not exert any cytotoxic effect on HL-60 cells. The M121C and T169M single mutants had reduced catalytic activities (nearly 2.5- to 4-fold vs wild type enzyme, respectively). Mutant Q63E, endowed with a similar catalytic efficiency versus asparagine and halved glutaminase efficiency with respect to the wild type enzyme, was able to exert a cytotoxic effect comparable to, or higher than, the one of the wild type enzyme when similar asparaginase units were used. These findings may be relevant to determine the role of glutaminase activity of L-asparaginase in the anti-proliferative effect of the drug and to shed light on how to engineer the best asparaginase/glutaminase combination for an ever improved, patients-tailored therapy.}, author = {Maggi, Maristella and Chiarelli, Laurent R. and Valentini, Giovanna and Scotti, Claudia}, doi = {10.1371/journal.pone.0117025}, journal = {PLoS ONE}, month = {feb}, pages = {e0117025}, title = {Engineering of Helicobacter pylori L-Asparaginase: Characterization of Two Functionally Distinct Groups of Mutants}, url = {https://doi.org/10.1371/journal.pone.0117025}, volume = {10}, year = {2015} } @article{Maggi2015_2, abstract = {Bacterial asparaginases (amidohydrolases, EC 3.5.1.1) are important enzymes in cancer therapy, especially for Acute Lymphoblastic Leukemia. They are tetrameric enzymes able to catalyze the deamination of L-ASN and, to a variable extent, of L-GLN, on which leukemia cells are dependent for survival. In contrast to other known L-asparaginases, Helicobacter pylori CCUG 17874 type II enzyme (HpASNase) is cooperative and has a low affinity towards L-GLN. In this study, some critical amino acids forming the active site of HpASNase (T16, T95 and E289) have been tackled by rational engineering in the attempt to better define their role in catalysis and to achieve a deeper understanding of the peculiar cooperative behavior of this enzyme. Mutations T16E, T95D and T95H led to a complete loss of enzymatic activity. Mutation E289A dramatically reduced the catalytic activity of the enzyme, but increased its thermostability. Interestingly, E289 belongs to a loop that is very variable in L-asparaginases from the structure, sequence and length point of view, and which could be a main determinant of their different catalytic features.}, author = {Maggi, Maristella and Chiarelli, Laurent R. and Valentini, Giovanna and Scotti, Claudia}, doi = {10.3390/biom5020306}, journal = {Biomolecules}, month = {mar}, pages = {306-317}, title = {Tackling Critical Catalytic Residues in Helicobacter pylori L-Asparaginase}, url = {http://dx.doi.org/10.3390/biom5020306}, volume = {5}, year = {2015} } @article{Meneghetti2016, abstract = {Tuberculosis nowadays ranks as the second leading cause of death from an infectious disease worldwide. In the last twenty years, this disease has again started to spread mainly for the appearance of multi-drug resistant forms. Therefore, new targets are needed to address the growing emergence of bacterial resistance and for antitubercular drug development. Efficient iron acquisition is crucial for the pathogenesis of Mycobacterium tuberculosis, because it serves as cofactor in many essential biological processes, including DNA biosynthesis and cellular respiration. Bacteria acquire iron chelating non-heme iron from the host using the siderophore mycobactins and carboxymycobactins and by the uptake of heme iron released by damaged red blood cells, through several acquisition systems. Drug discovery focused its efforts in the discovery of MbtI and MbtA inhibitors, which are two enzymes involved in the mycobactin biosynthetic pathway. In particular, MbtI inhibitors have been studied in vitro, while MbtA inhibitors showed activity also in infected mice. Another class of compounds, MmpL3 inhibitors, showed antitubercular activity in vitro and in vivo, but their mechanism of action seems to be off-target. Some compounds inhibiting 4’-phosphopantetheinyl transferase were discovered but not tested on in vivo assays. The available data reported here based on inhibitors and gene deletion studies, suggest that targeting iron acquisition systems could be considered a promising antitubercular strategy. Due to their redundancy, the relative importance of each pathway for Mycobacterium tuberculosis survival has still to be determined. Thus, in vivo studies with new, potent and specific inhibitors are needed to highlight target selection.}, author = {Meneghetti, Fiorella and Villa, Stefania and Gelain, Arianna and Barlocco, Daniela and Chiarelli, L. and Roberto Chiarelli, Laurent and Pasca, M. and Rosalia Pasca, Maria and Costantino, Luca}, doi = {10.2174/0929867323666160607223747}, journal = {Current Medicinal Chemistry}, month = {jan}, pages = {4009-4026}, title = {Iron acquisition pathways as targets for antitubercular drugs}, url = {https://oadoi.org/10.2174/0929867323666160607223747}, volume = {23}, year = {2016} } @article{Mori2015, abstract = {To combat the emergence of drug-resistant strains of Mycobacterium tuberculosis, new antitubercular agents and novel drug targets are needed. Phenotypic screening of a library of 594 hit compounds uncovered two leads that were active against M. tuberculosis in its replicating, non-replicating, and intracellular states: compounds 7947882 (5-methyl-N-(4-nitrophenyl)thiophene-2-carboxamide) and 7904688 (3-phenyl-N-[(4-piperidin-1-ylphenyl)carbamothioyl]propanamide). Mutants resistant to both compounds harbored mutations in ethA (rv3854c), the gene encoding the monooxygenase EthA, and/or in pyrG (rv1699) coding for the CTP synthetase, PyrG. Biochemical investigations demonstrated that EthA is responsible for the activation of the compounds, and by mass spectrometry we identified the active metabolite of 7947882, which directly inhibits PyrG activity. Metabolomic studies revealed that pharmacological inhibition of PyrG strongly perturbs DNA and RNA biosynthesis, and other metabolic processes requiring nucleotides. Finally, the crystal structure of PyrG was solved, paving the way for rational drug design with this newly validated drug target. ; Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) ; Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) ; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)}, author = {Mori, Giorgia and Chiarelli, Laurent R. and Esposito, Marta and Makarov, Vadim and Bellinzoni, Marco and Hartkoorn, Ruben C. and Degiacomi, Giulia and Boldrin, Francesca and Ekins, Sean and de Jesus Lopes Ribeiro, Ana Luisa and Ribeiro, Ana Luisa de Jesus Lopes and Marino, Leonardo B. and Centárová, Ivana and Svetlíková, Zuzana and Blaško, Jaroslav and Kazakova, Elena and Lepioshkin, Alexander and Barilone, Nathalie and Zanoni, Giuseppe and Porta, Alessio and Fondi, Marco and Fani, Renato and Baulard, Alain R. and Mikušová, Katarína and Alzari, Pedro M. and de Carvalho, Luiz Pedro S. and Manganelli, Riccardo and Carvalho, Luiz Pedro S. de and Riccardi, Giovanna and Cole, Stewart T. and Pasca, Maria Rosalia}, doi = {10.1016/j.chembiol.2015.05.016}, journal = {Chemistry and Biology}, month = {jun}, pages = {917-927}, title = {Thiophenecarboxamide Derivatives Activated by EthA Kill Mycobacterium tuberculosis by Inhibiting the CTP Synthetase PyrG}, url = {https://doi.org/10.1016/j.chembiol.2015.05.016}, volume = {22}, year = {2015} } @article{Mori2017, author = {Mori, Giorgia and Chiarelli, Laurent Roberto and Riccardi, Giovanna and Pasca, Maria Rosalia}, doi = {10.1016/j.drudis.2016.09.006}, journal = {Drug Discovery Today}, month = {mar}, pages = {519-525}, title = {New prodrugs against tuberculosis}, url = {https://oadoi.org/10.1016/j.drudis.2016.09.006}, volume = {22}, year = {2017} } @article{Naik2014, author = {Naik, Maruti and Humnabadkar, Vaishali and Tantry, Subramanyam J. and Panda, Manoranjan and Narayan, Ashwini and Guptha, Supreeth and Panduga, Vijender and Manjrekar, Praveena and Jena, Lalit kumar and Koushik, Krishna and Shanbhag, Gajanan and Jatheendranath, Sandesh and Manjunatha, M. R. and Gorai, Gopinath and Bathula, Chandramohan and Rudrapatna, Suresh and Achar, Vijayashree and Sharma, Sreevalli and Ambady, Anisha and Hegde, Naina and Mahadevaswamy, Jyothi and Kaur, Parvinder and Sambandamurthy, Vasan K. and Awasthy, Disha and Narayan, Chandan and Ravishankar, Sudha and Madhavapeddi, Prashanti and Reddy, Jitendar and Prabhakar, Kr and Saralaya, Ramanatha and Chatterji, Monalisa and Whiteaker, James and McLaughlin, Bob and Chiarelli, Laurent R. and Riccardi, Giovanna and Pasca, Maria Rosalia and Binda, Claudia and Neres, João and Dhar, Neeraj and Signorino-Gelo, François and McKinney, John D. and Ramachandran, Vasanthi and Shandil, Radha and Tommasi, Ruben and Iyer, Pravin S. and Narayanan, Shridhar and Hosagrahara, Vinayak and Kavanagh, Stefan and Dinesh, Neela and Ghorpade, Sandeep R.}, doi = {10.1021/jm5005978}, journal = {Journal of Medicinal Chemistry}, month = {jun}, pages = {5419-5434}, title = {4-Aminoquinolone Piperidine Amides: Noncovalent Inhibitors of DprE1 with Long Residence Time and Potent Antimycobacterial Activity}, url = {https://oadoi.org/10.1021/jm5005978}, volume = {57}, year = {2014} } @article{Oliveira2017, author = {Oliveira, Paulo F. M. and Guidetti, Brigitte and Chamayou, Alain and Madacki, Jan and André-Barrès, Christiane and Korduláková, Jana and Mori, Giorgia and Orena, Beatrice S. and Chiarelli, Laurent R. and Pasca, Maria R. and Lherbet, Christian and Carayon, Chantal and Massou, Stéphane and Baron, Michel and Baltas, Michel and Filho Marques de Oliveira, Paulo}, doi = {10.3390/molecules22091457}, journal = {Molecules}, month = {sep}, pages = {1457}, title = {Mechanochemical Synthesis and Biological Evaluation of Novel Isoniazid Derivatives with Potent Antitubercular Activity}, url = {https://doi.org/10.3390/molecules22091457}, volume = {22}, year = {2017} } @article{Pini2018, author = {Pini, Elena and Poli, Giulio and Tuccinardi, Tiziano and Chiarelli, Laurent and Mori, Matteo and Gelain, Arianna and Costantino, Luca and Villa, Stefania and Meneghetti, Fiorella and Barlocco, Daniela}, doi = {10.3390/molecules23071506}, journal = {Molecules}, month = {jun}, pages = {1506}, title = {New Chromane-Based Derivatives as Inhibitors of Mycobacterium tuberculosis Salicylate Synthase (MbtI): Preliminary Biological Evaluation and Molecular Modeling Studies}, url = {https://doi.org/10.3390/molecules23071506}, volume = {23}, year = {2018} } @article{Roberto Chiarelli2016, author = {Roberto Chiarelli, Laurent and Mori, Giorgia and Esposito, Marta and Silvia Orena, Beatrice and Rosalia Pasca, Maria}, doi = {10.2174/1389557516666160831164925}, journal = {Current Medicinal Chemistry}, month = {nov}, pages = {3813-3846}, title = {New and Old Hot Drug Targets in Tuberculosis}, url = {https://oadoi.org/10.2174/1389557516666160831164925}, volume = {23}, year = {2016} } @article{Sala2020, abstract = {Mycobacterium tuberculosis, the etiological agent of human tuberculosis (TB), represents a global challenge to human health since it is the main cause of death by an infectious disease worldwide [...]}, author = {Sala, Claudia and Chiarelli, Laurent Roberto and Riccardi, Giovanna}, doi = {10.3390/app10176069}, journal = {Applied Sciences}, month = {sep}, pages = {6069}, title = {Editorial on Special Issue “Tuberculosis Drug Discovery and Development 2019”}, url = {https://doi.org/10.3390/app10176069}, volume = {10}, year = {2020} } @article{Scoffone2016, abstract = {AbstractBurkholderia cenocepacia, an opportunistic respiratory pathogen particularly relevant for cystic fibrosis patients, is difficult to eradicate due to its high level of resistance to most clinically relevant antimicrobials. Consequently, the discovery of new antimicrobials as well as molecules capable of inhibiting its virulence is mandatory. In this regard quorum sensing (QS) represents a good target for anti-virulence therapies, as it has been linked to biofilm formation and is important for the production of several virulence factors, including proteases and siderophores. Here, we report the discovery of new diketopiperazine inhibitors of the B. cenocepacia acyl homoserine lactone synthase CepI, and report their anti-virulence properties. Out of ten different compounds assayed against recombinant CepI, four were effective inhibitors, with IC50 values in the micromolar range. The best compounds interfered with protease and siderophore production, as well as with biofilm formation, and showed good in vivo activity in a Caenorhabditis elegans infection model. These molecules were also tested in human cells and showed very low toxicity. Therefore, they could be considered for in vivo combined treatments with established or novel antimicrobials, to improve the current therapeutic strategies against B. cenocepacia.}, author = {Scoffone, Viola C. and Chiarelli, Laurent R. and Makarov, Vadim and Brackman, Gilles and Israyilova, Aygun and Azzalin, Alberto and Forneris, Federico and Riabova, Olga and Savina, Sventlana and Coenye, Tom and Riccardi, Giovanna and Buroni, Silvia}, doi = {10.1038/srep32487}, journal = {Scientific Reports}, month = {jan}, title = {Discovery of new diketopiperazines inhibiting Burkholderia cenocepacia quorum sensing in vitro and in vivo}, url = {https://doi.org/10.1038/srep32487}, volume = {6}, year = {2016} } @article{Scoffone2017, author = {Scoffone, Viola C. and Chiarelli, Laurent R. and Trespidi, Gabriele and Mentasti, Massimo and Riccardi, Giovanna and Buroni, Silvia}, doi = {10.3389/fmicb.2017.01592}, journal = {Frontiers in Microbiology}, month = {aug}, title = {Burkholderia cenocepacia Infections in Cystic Fibrosis Patients: Drug Resistance and Therapeutic Approaches}, url = {https://doi.org/10.3389/fmicb.2017.01592}, volume = {8}, year = {2017} } @article{Spadaro2016, author = {Spadaro, Francesca and Scoffone, Viola C. and Chiarelli, Laurent R. and Fumagalli, Marco and Buroni, Silvia and Riccardi, Giovanna and Forneris, Federico}, doi = {10.1021/acs.biochem.6b00178}, journal = {Biochemistry}, month = {jun}, pages = {3241-3250}, title = {The Crystal Structure of Burkholderia cenocepacia DfsA Provides Insights into Substrate Recognition and Quorum Sensing Fatty Acid Biosynthesis}, url = {https://oadoi.org/10.1021/acs.biochem.6b00178}, volume = {55}, year = {2016} } @article{Tiwari2016, author = {Tiwari, Rohit and Miller, Patricia A. and Chiarelli, Laurent R. and Mori, Giorgia and Šarkan, Michal and Centárová, Ivana and Cho, Sanghyun and Mikušová, Katarína and Franzblau, Scott G. and Oliver, Allen G. and Miller, Marvin J.}, doi = {10.1021/acsmedchemlett.5b00424}, journal = {ACS Medicinal Chemistry Letters}, month = {jan}, pages = {266-270}, title = {Design, Syntheses, and Anti-TB Activity of 1,3-Benzothiazinone Azide and Click Chemistry Products Inspired by BTZ043}, url = {http://europepmc.org/articles/pmc4789662?pdf=render}, volume = {7}, year = {2016} } @incollection{Viglio2018, author = {Viglio, Simona and Cagnone, Maddalena and Chiarelli, Laurent Roberto and Salvini, Roberta and Iadarola, Paolo}, doi = {10.5772/intechopen.75042}, journal = {Electrophoresis - Life Sciences Practical Applications}, month = {sep}, title = {The Role of One- and Two-Dimensional Electrophoretic Techniques in Proteomics of the Lung}, url = {https://doi.org/10.5772/intechopen.75042}, year = {2018} }