Antonio Del Rio Flores

All Publications

• Characterization of the Flavin-Dependent Monooxygenase Involved in the Biosynthesis of the Nocardiosis-Associated Polyketide†. Biochemistry Del Rio Flores, A., Khosla, C. 2024

  Abstract

  Some species of the Nocardia genus harbor a highly conserved biosynthetic gene cluster designated as the NOCardiosis-Associated Polyketide (NOCAP) synthase that produces a unique glycolipid natural product. The NOCAP glycolipid is composed of a fully substituted benzaldehyde headgroup linked to a polyfunctional alkyl tail and an O-linked disaccharide composed of 3-α-epimycarose and 2-O-methyl-α-rhamnose. Incorporation of the disaccharide unit is preceded by a critical step involving hydroxylation by NocapM, a flavin monooxygenase. In this study, we employed biochemical, spectroscopic, and kinetic analyses to explore the substrate scope of NocapM. Our findings indicate that NocapM catalyzes hydroxylation of diverse aromatic substrates, although the observed coupling between NADPH oxidation and substrate hydroxylation varies widely from substrate to substrate. Our in-depth biochemical characterization of NocapM provides a solid foundation for future mechanistic studies of this enzyme as well as its utilization as a practical biocatalyst.

  View details for DOI 10.1021/acs.biochem.4c00480

  View details for PubMedID 39433512

• AI is a viable alternative to high throughput screening: a 318-target study SCIENTIFIC REPORTS Wallach, I., Bernard, D., Nguyen, K., Ho, G., Morrison, A., Stecula, A., Rosnik, A., O'Sullivan, A., Davtyan, A., Samudio, B., Thomas, B., Worley, B., Butler, B., Laggner, C., Thayer, D., Moharreri, E., Friedland, G., Truong, H., van den Bedem, H., Ng, H., Stafford, K., Sarangapani, K., Giesler, K., Ngo, L., Mysinger, M., Ahmed, M., Anthis, N. J., Henriksen, N., Gniewek, P., Eckert, S., de Oliveira, S., Suterwala, S., PrasadPrasad, S., Shek, S., Contreras, S., Hare, S., Palazzo, T., O'Brien, T. E., Van Grack, T., Williams, T., Chern, T., Kenyon, V., Lee, A. H., Cann, A. B., Bergman, B., Anderson, B. M., Cox, B. D., Warrington, J. M., Sorenson, J. M., Goldenberg, J. M., Young, M. A., DeHaan, N., Pemberton, R. P., Schroedl, S., Abramyan, T. M., Gupta, T., Mysore, V., Presser, A. G., Ferrando, A. A., Andricopulo, A. D., Ghosh, A., Ayachi, A., Mushtaq, A., Shaqra, A. M., Toh, A., Smrcka, A. V., Ciccia, A., de Oliveira, A., Sverzhinsky, A., de Sousa, A., Agoulnik, A. I., Kushnir, A., Freiberg, A. N., Statsyuk, A. V., Gingras, A. R., Degterev, A., Tomilov, A., Vrielink, A., Garaeva, A. A., Bryant-Friedrich, A., Caflisch, A., Patel, A. K., Rangarajan, A., Matheeussen, A., Battistoni, A., Caporali, A., Chini, A., Ilari, A., Mattevi, A., Foote, A., Trabocchi, A., Stahl, A., Herr, A. B., Berti, A., Freywald, A., Reidenbach, A. G., Lam, A., Cuddihy, A. R., White, A., Taglialatela, A., Ojha, A. K., Cathcart, A. M., Motyl, A. L., Borowska, A., D'Antuono, A., Hirsch, A. H., Porcelli, A., Minakova, A., Montanaro, A., Mueller, A., Fiorillo, A., Virtanen, A., O'Donoghue, A. J., Flores, A., Garmendia, A. E., Pineda-Lucena, A., Panganiban, A. T., Samantha, A., Chatterjee, A. K., Haas, A. L., Paparella, A. S., John, A., Prince, A., ElSheikh, A., Apfel, A., Colomba, A., O'Dea, A., Diallo, B., Ribeiro, B., Bailey-Elkin, B. A., Edelman, B. L., Liou, B., Perry, B., Chua, B., Kovats, B., Englinger, B., Balakrishnan, B., Gong, B., Agianian, B., Pressly, B., Salas, B., Duggan, B. M., Geisbrecht, B. V., Dymock, B. W., Morten, B. C., Hammock, B. D., Mota, B., Dickinson, B. C., Fraser, C., Lempicki, C., Novina, C. D., Torner, C., Ballatore, C., Bon, C., Chapman, C. J., Partch, C. L., Chaton, C. T., Huang, C., Yang, C., Kahler, C. M., Karan, C., Keller, C., Dieck, C. L., Chen Huimei, Liu, C., Peltier, C., Mantri, C., Kemet, C., Mueller, C. E., Weber, C., Zeina, C. M., Muli, C. S., Morisseau, C., Alkan, C., Reglero, C., Loy, C. A., Wilson, C. M., Myhr, C., Arrigoni, C., Paulino, C., Santiago, C., Luo, D., Tumes, D. J., Keedy, D. A., Lawrence, D. A., Chen, D., Manor, D., Trader, D. J., Hildeman, D. A., Drewry, D. H., Dowling, D. J., Hosfield, D. J., Smith, D. M., Moreira, D., Siderovski, D. P., Shum, D., Krist, D. T., Riches, D. H., Ferraris, D., Anderson, D. H., Coombe, D. R., Welsbie, D. S., Hu, D., Ortiz, D., Alramadhani, D., Zhang, D., Chaudhuri, D., Slotboom, D. J., Ronning, D. R., Lee, D., Dirksen, D., Shoue, D. A., Zochodne, D., Krishnamurthy, D., Duncan, D., Glubb, D. M., Gelardi, E., Hsiao, E. C., Lynn, E. G., Silva, E., Aguilera, E., Lenci, E., Abraham, E., Lama, E., Mameli, E., Leung, E., Christensen, E. M., Mason, E. R., Petretto, E., Trakhtenberg, E. F., Rubin, E. J., Strauss, E., Thompson, E. W., Cione, E., Lisabeth, E., Fan, E., Kroon, E., Jo, E., Garcia-Cuesta, E. M., Glukhov, E., Gavathiotis, E., Yu, F., Xiang, F., Leng, F., Wang, F., Ingoglia, F., van den Akker, F., Borriello, F., Vizeacoumar, F. J., Luh, F., Buckner, F. S., Vizeacoumar, F. S., Ben Bdira, F., Svensson, F., Rodriguez, G., Bognar, G., Lembo, G., Zhang, G., Dempsey, G., Eitzen, G., Mayer, G., Greene, G. L., Garcia, G. A., Lukacs, G. L., Prikler, G., Parico, G. G., Colotti, G., De Keulenaer, G., Cortopassi, G., Roti, G., Girolimetti, G., Fiermonte, G., Gasparre, G., Leuzzi, G., Dahal, G., Michlewski, G., Conn, G. L., Stuchbury, G., Bowman, G. R., Popowicz, G., Veit, G., de Souza, G., Akk, G., Caljon, G., Alvarez, G., Rucinski, G., Lee, G., Cildir, G., Li, H., Breton, H. E., Jafar-Nejad, H., Zhou, H., Moore, H. P., Tilford, H., Yuan, H., Shim, H., Wulff, H., Hoppe, H., Chaytow, H., Tam, H., Van Remmen, H., Xu, H., Debonsi, H., Lieberman, H. B., Jung, H., Fan, H., Feng, H., Zhou, H., Kim, H., Greig, I. R., Caliandro, I., Corvo, I., Arozarena, I., Mungrue, I. N., Verhamme, I. M., Qureshi, I., Lotsaris, I., Cakir, I., Perry, J. P., Kwiatkowski, J., Boorman, J., Ferreira, J., Fries, J., Kratz, J., Miner, J., Siqueira-Neto, J. L., Granneman, J. G., Ng, J., Shorter, J., Voss, J., Gebauer, J. M., Chuah, J., Mousa, J. J., Maynes, J. T., Evans, J. D., Dickhout, J., MacKeigan, J. P., Jossart, J. N., Zhou, J., Lin, J., Xu, J., Wang, J., Zhu, J., Liao, J., Xu, J., Zhao, J., Lin, J., Lee, J., Reis, J., Stetefeld, J., Bruning, J. B., Bruning, J., Coles, J. G., Tanner, J. J., Pascal, J. M., So, J., Pederick, J. L., Costoya, J. A., Rayman, J. B., Maciag, J. J., Nasburg, J., Gruber, J. J., Finkelstein, J. M., Watkins, J., Rodriguez-Frade, J., Arias, J., Lasarte, J., Oyarzabal, J., Milosavljevic, J., Cools, J., Lescar, J., Bogomolovas, J., Wang, J., Kee, J., Kee, J., Liao, J., Sistla, J. C., Abrahao, J., Sishtla, K., Francisco, K. R., Hansen, K. B., Molyneaux, K. A., Cunningham, K. A., Martin, K. R., Gadar, K., Ojo, K. K., Wong, K. S., Wentworth, K. L., Lai, K., Lobb, K. A., Hopkins, K. M., Parang, K., Machaca, K., Pham, K., Ghilarducci, K., Sugamori, K. S., McManus, K., Musta, K., Faller, K. E., Nagamori, K., Mostert, K. J., Korotkov, K. V., Liu, K., Smith, K. S., Sarosiek, K., Rohde, K. H., Kim, K., Lee, K., Pusztai, L., Lehtio, L., Haupt, L. M., Cowen, L. E., Byrne, L. J., Su, L., Wert-Lamas, L., Puchades-Carrasco, L., Chen, L., Malkas, L. H., Zhuo, L., Hedstrom, L., Hedstrom, L., Walensky, L. D., Antonelli, L., Iommarini, L., Whitesell, L., Randall, L. M., Fathallah, M., Nagai, M., Kilkenny, M., Ben-Johny, M., Lussier, M. P., Windisch, M. P., Lolicato, M., Lolli, M., Vleminckx, M., Caroleo, M., Macias, M. J., Valli, M., Barghash, M. M., Mellado, M., Tye, M. A., Wilson, M. A., Hannink, M., Ashton, M. R., dela Cerna, M. C., Giorgis, M., Safo, M. K., St Maurice, M., McDowell, M., Pasquali, M., Mehedi, M., Serafim, M., Soellner, M. B., Alteen, M. G., Champion, M. M., Skorodinsky, M., O'Mara, M. L., Bedi, M., Rizzi, M., Levin, M., Mowat, M., Jackson, M. R., Paige, M., Al-Yozbaki, M., Giardini, M. A., Maksimainen, M. M., De Luise, M., Hussain, M., Christodoulides, M., Stec, N., Zelinskaya, N., Van Pelt, N., Merrill, N. M., Singh, N., Kootstra, N. A., Singh, N., Gandhi, N. S., Chan, N., Trinh, N., Schneider, N. O., Matovic, N., Horstmann, N., Longo, N., Bharambe, N., Rouzbeh, N., Mahmoodi, N., Gumede, N., Anastasio, N. C., Ben Khalaf, N., Rabal, O., Kandror, O., Escaffre, O., Silvennoinen, O., Bishop, O., Iglesias, P., Sobrado, P., Chuong, P., O'Connell, P., Martin-Malpartida, P., Mellor, P., Fish, P. V., Moreira, P., Zhou, P., Liu, P., Liu, P., Wu, P., Agogo-Mawuli, P., Jones, P. L., Ngoi, P., Toogood, P., Ip, P., von Hundelshausen, P., Lee, P. H., Rowswell-Turner, R. B., Balana-Fouce, R., Rocha, R., Guido, R. C., Ferreira, R., Agrawal, R. K., Harijan, R. K., Ramachandran, R., Verma, R., Singh, R. K., Tiwari, R., Mazitschek, R., Koppisetti, R. K., Dame, R. T., Douville, R. N., Austin, R. C., Taylor, R. E., Moore, R. G., Ebright, R. H., Angell, R. M., Yan, R., Kejriwal, R., Batey, R. A., Blelloch, R., Vandenberg, R. J., Hickey, R. J., Kelm, R. J., Lake, R. J., Bradley, R. K., Blumenthal, R. M., Solano, R., Gierse, R., Viola, R. E., McCarthy, R. R., Reguera, R., Uribe, R., do Monte-Neto, R., Gorgoglione, R., Cullinane, R. T., Katyal, S., Hossain, S., Phadke, S., Shelburne, S. A., Geden, S. E., Johannsen, S., Wazir, S., Legare, S., Landfear, S. M., Radhakrishnan, S. K., Ammendola, S., Dzhumaev, S., Seo, S., Li, S., Zhou, S., Chu, S., Chauhan, S., Maruta, S., Ashkar, S. R., Shyng, S., Conticello, S. G., Buroni, S., Garavaglia, S., White, S. J., Zhu, S., Tsimbalyuk, S., Chadni, S., Byun, S., Park, S., Xu, S. Q., Banerjee, S., Zahler, S., Espinoza, S., Gustincich, S., Sainas, S., Celano, S. L., Capuzzi, S. J., Waggoner, S. N., Poirier, S., Olson, S. H., Marx, S. O., Van Doren, S. R., Sarilla, S., Brady-Kalnay, S. M., Dallman, S., Azeem, S., Teramoto, T., Mehlman, T., Swart, T., Abaffy, T., Akopian, T., Haikarainen, T., Moreda, T., Ikegami, T., Teixeira, T., Jayasinghe, T. D., Gillingwater, T. H., Kampourakis, T., Richardson, T. I., Herdendorf, T. J., Kotze, T. J., O'Meara, T. R., Corson, T. W., Hermle, T., Ogunwa, T., Lan, T., Su, T., Banjo, T., O'Mara, T. A., Chou, T., Chou, T., Baumann, U., Desai, U. R., Pai, V. P., Thai, V., Tandon, V., Banerji, V., Robinson, V. L., Gunasekharan, V., Namasivayam, V., Segers, V. M., Maranda, V., Dolce, V., Maltarollo, V., Scoffone, V., Woods, V. A., Ronchi, V., Le, V., Clayton, W., Lowther, W., Houry, W. A., Li, W., Tang, W., Zhang, W., Van Voorhis, W. C., Donaldson, W. A., Hahn, W. C., Kerr, W. G., Gerwick, W. H., Bradshaw, W. J., Foong, W., Blanchet, X., Wu, X., Lu, X., Qi, X., Xu, X., Yu, X., Qin, X., Wang, X., Yuan, X., Zhang, X., Zhang, Y., Hu, Y., Aldhamen, Y., Chen, Y., Li, Y., Sun, Y., Zhu, Y., Gupta, Y. K., Perez-Pertejo, Y., Li, Y., Tang, Y., He, Y., Tse-Dinh, Y., Sidorova, Y. A., Yen, Y., Li, Y., Frangos, Z. J., Chung, Z., Su, Z., Wang, Z., Zhang, Z., Liu, Z., Inde, Z., Artia, Z., Heifets, A., Atomwise AIMS Program 2024; 14 (1): 7526

  Abstract

  High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.

  View details for DOI 10.1038/s41598-024-54655-z

  View details for Web of Science ID 001253148000001

  View details for PubMedID 38565852

  View details for PubMedCentralID PMC10987645

• Discovery and Characterization of the Fully Decorated Nocardiosis-Associated Polyketide Natural Product. Journal of the American Chemical Society Kishore, S., Del Rio Flores, A., Lynch, S. R., Yuet, K. P., Khosla, C. 2024

  Abstract

  The genomes of 40 strains of Nocardia, most of which were associated with life-threatening human infections, encode a highly conserved assembly line polyketide synthase designated as the NOCAP (NOCardiosis-Associated Polyketide) synthase, whose product structure has been previously described. Here we report the structure and inferred biosynthetic pathway of the fully decorated glycolipid natural product. Its structure reveals a fully substituted benzaldehyde headgroup harboring an unusual polyfunctional tail and an O-linked disaccharide comprising a 3-α-epimycarose and 2-O-methyl-α-rhamnose whose installation requires flavin monooxygenase-dependent hydroxylation of the polyketide product. Production of the fully decorated glycolipid was verified in cultures of two patient-derived Nocardia species. In both E. coli and Nocardia spp., the glycolipid was only detected in culture supernatants, consistent with data from genetic knockout experiments implicating roles for two dedicated proteins in installing the second sugar substituent only after the monoglycosyl intermediate is exported across the bacterial cell membrane. With the NOCAP product in hand, the stage is set for investigating the evolutionary benefit of this polyketide biosynthetic pathway for Nocardia strains capable of infecting human hosts.

  View details for DOI 10.1021/jacs.3c13670

  View details for PubMedID 38295028