DigiChem Lab

For citation analyses and h-index check Google Scholar.


2022

70. Chemoproteomics-Enabled Identification of 4-Oxo-β-Lactams as Inhibitors of Dipeptidyl Peptidases 8 and 9
L. A. R. Carvalho, B. Ross, L. Fehr, O. Bolgi, S. Wöhrle, K. M. Lum, D. Podlesainski, A. C. Vieira, R. Kiefersauer, R. Félix, T. Rodrigues, S. D. Lucas, O. Groß, R. Geiss-Friedlander, B. F. Cravatt, R. Huber, M. Kaiser, R. Moreira
Angew Chem Int Ed 2022, accepted




69. A Special issue on artificial intelligence for drug discovery
T. Rodrigues*
Bioorg Med Chem 2022, 70, 116939




68. Controlled masking and targeted release of redox-cycling ortho-quinones via a C–C bond-cleaving 1,6-elimination
L. Dunsmore, C. D. Navo, J. Becher, E. G. de Montes, A. Guerreiro, E. Hoyt , L. Brown, V. Zelenay, S. Mikutis, J. Cooper, I. Barbieri, S. Lawrinowitz, E. Siouve, E. Martin, P. R. Ruivo, T. Rodrigues, F. P. da Cruz, O. Werz, G. Vassiliou, P. Ravn, G. Jiménez-Osés, G. J. L. Bernardes
Nat Chem 2022, 14, 754-765

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67. Evaluation guidelines for machine learning tools in the chemical sciences
A. Bender, N. Schneider, M. Segler, W. P. Walters, O. Engkvist, T. Rodrigues*
Nat Rev Chem 2022, 6, 428-442

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66. Nuisance small molecules under a machine-learning lens
T. Rodrigues*
Digital Discov 2022, 1, 209-2015

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65. Deriving intuition in catalyst design with machine learning
T. Rodrigues*
Chem 2022, 8, 15-19

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2021

64. Machine learning for next generation nanotechlonology in healthcare
A. Lorenc, B. B. Mendes, J. Conniot, D. P. Sousa, J. Conde*, T. Rodrigues*
Matter 2021, 4, 3078-3080

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63. Exploration of long-chain vitamin E metabolites for the discovery of a highly potent, orally effective and metabolically stable 5-LOX inhibitor that limits inflammation
K. Neukirch, K. Alsabil, C.-P. Dinh, R. Bilancia, M Raasch, A. Ville, I. Cerqua, G. Viault, D. Bréard, S. Pace, V. Temml, E. Brunner, P. Jordan, M. Marques, K. Loeser, A. Gollowitzer, S. Permann, J. Gerstmeier, S. Lorkowski, H. Stuppner, U. Garscha, T. Rodrigues, G. Bernardes, D. Schuster, D. Seraphin, P. Richomme, A. Rossi, A. S. Mosig, F. Roviezzo, O. Werz, J.-J. Helesbeux, A Koeberle
J. Med. Chem. 2021, 64, 11496-11526

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62. Facts and Figures on Materials Science and Nanotechnology Progress and Investment
S. Talebian*, T. Rodrigues*, J. das Neves, B. Sarmento, R. Langer, J. Conde
ACS Nano 2021, 15, 15940-15952

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61. Augmenting adaptive machine learning with kinetic modelling for reaction optimization
A. F. Almeida, F. A. P. Ataíde*, R. M. S. Loureiro, R. Moreira, T. Rodrigues*
J. Org. Chem. 2021, 86, 14192-14198

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60. Combating small molecule aggregation with machine learning
K. Lee, A. Yang, Y.-C. Lin*, D. Reker, G. J. L. Bernardes, T. Rodrigues*
Cell Rep. Phys. Sci. 2021, 2, 100573

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59. Allosteric Antagonist Modulation of TRPV2 by Piperlongumine Impairs Glioblastoma Progression
J. Conde*, R. A. Pumroy*, C. Baker*, T. Rodrigues*, A. Guerreiro, B. B. Sousa, M. C. Marques, B. P. de Almeida, S. Lee, E. P. Leites, D. Picard, A. Samanta, S. H. Vaz, F. Sieglitz, M. Langini, M. Remke, R. Roque, T. Weiss, M. Weller, Y. Liu, S. Han, F. Corzana, V. A. Morais, C. C. Faria, T. Carvalho, P. Filippakopoulos, B. Snijder, N. L. Barbosa-Morais, V. Y. Moiseenkova-Bell, Gonçalo J. L. Bernardes
ACS Cent. Sci. 2021, 7, 868-881

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2020

58. Adaptive optimization of chemical reactions with minimal experimental information
D. Reker, Emily A. Hoyt, G. J. L. Bernardes*, T. Rodrigues*
Cell Rep. Phys. Sci. 2020, 1, 100247


57. Structural and biophysical insights of the mode of covalent binding of rationally designed potent BMX inhibitors
J. D. Seixas, B. B. Sousa, M. C. Marques, A. Guerreiro, R. Traquete, T. Rodrigues, I. S. Albuquerque, M. Sousa, A. R. Lemos, P. M. F. Sousa, T. M. Bandeiras, D. Wu, S. K. Doyle, C. V. Robinson, A. N. Koehler, F. Corzana, P. M. Matias, G. J. L. Bernardes
RSC Chem Biol 2020, 1, 251-262


56. The good, the bad, and the ugly in chemical and biological data for machine learning
T. Rodrigues*
Drug Discov. Today: Technol. 2019, 32-33, 3-8


55. The antidiabetic drug lobeglitazone has the potential to inhibit PTP1B activity
R. F. Rocha, T. Rodrigues, A. C. O. Menegatti, G. J. L. Bernardes, H. Terenzi
Bioorg. Chem. 2020, 100, 103927


54. Brain-sparing sympathofacilitators mitigate obesity without adverse cardiovascular effects
I. Mahú, A. Barateiro, E. Rial-Pensado, N. Martinéz-Sánchez, S. H. Vaz, P. M. S. D. Cal, B. Jenkins, T. Rodrigues, C. Cordeiro, M. F. Costa, R. Mendes, E. Seixas, M. M. A. Pereira, N. Kubasova, V. Gres, I. Morris, C. Temporão, M. Olivares, Y. Sanz, A. Koulman, F. Corzana, A. M. Sebastião, M. López, G. J. L. Bernardes, A. I. Domingos
Cell Metab. 2020, 31, 1120-1135


53. Machine learning for target discovery in drug development
T. Rodrigues*, G. J. L. Bernardes*
Curr. Opin. Chem. Biol. 2020, 56, 16-22


2019

52. Evaluation of linker length effects on a BET bromodomain probe
R. Traquete, E. Henderson, S. Picaud, P. M. S. D. Cal, F. Sieglitz, T. Rodrigues, R. Oliveira, P. Filippakopoulus, G. J. L. Bernardes
Chem. Commun. 2019, 55, 10128-10131


51. Synthetic organic chemistry driven by artificial intelligence
A. Filipa de Almeida, R. Moreira, T. Rodrigues*
Nat. Rev. Chem. 2019, 3, 589-604

50. Dissecting celastrol with machine learning to unveil dark pharmacology
T. Rodrigues*, B. P. de Almeida, N. L. Barbosa-Morais, G. J. L. Bernardes*
Chem. Commun. 2019, 55, 6369-6372

49. Natural product–drug conjugates for modulation of TRPV1-expressing tumors
C. Baker, T. Rodrigues, B. P. de Almeida, N. Barbosa-Morais, G. J. L. Bernardes
Bioorg. Med. Chem. 2019, 27, 2531-2536

48. Computational advances in combating colloidal aggregation in drug discovery
D. Reker*, G. J. L. Bernardes, T. Rodrigues*
Nat. Chem. 2019, 11, 402-418


2018

47. Discovery of 2,4-dimethoxypyridines as novel autophagy inhibitors
L. Robke, T. Rodrigues, P. Schröder, D. J. Foley, G. J. L. Bernardes, L. Laraia, H. Waldmann
Tetrahedron 2018, 74, 4531-4537

46. Machine intelligence decrypts β-lapachone as an allosteric 5-lipoxygenase inhibitor
T. Rodrigues*, M. Werner, J. Roth, E. H. G. da Cruz, M. C. Marques, S. A. Lobo, A. Koeberle, F. Corzana, E. N. da Silva Júnior, O. Werz, G. J. L. Bernardes*
Chem. Sci. 2018, 9, 6899-6903

45. Development of antibody-directed therapies: quo vadis?
T. Rodrigues*, G. J. L. Bernardes*
Angew. Chem. Int. Ed. 2018, 57, 2032-2034


2017

44. Chemoselective installation of amine bonds on proteins through aza-Michael ligation
A. Freedy, M. Matos, O. Boutureira, F. Corzana, A. Guerreiro, P. Akkapeddi, V. Somovilla, T. Rodrigues, K. Nicholls, B. Xie, G. Jiménez-Osés, K. Brindle, A. Neves, G. Bernardes
J. Am. Chem. Soc. 2017, 139, 18365-18375

43. Harnessing the potential of natural products in drug discovery from a cheminformatics vantage point
T. Rodrigues*
Org. Biomol. Chem. 2017, 15, 9275-9282

42. A Water-Bridged Cysteine-Cysteine Redox Regulation Mechanism in Bacterial Protein Tyrosine Phosphatases
J. B. Bertoldo, T. Rodrigues, L. Dunsmore, F. A. Aprile, M. C. Marques, L. Rosado, O. Boutureira, T. B. Steinbrecher, W. Sherman, F. Corzana, H. Terenzi, G. J. L. Bernardes
Chem 2017, 3, 665-677

41. Vinyl ether/tetrazine pair for the traceless release of alcohols in cells
E. Jiménez-Moreno, Z. Guo, B. L. Oliveira, I. S. Albuquerque, A. Kitowski, A. Guerreiro, O. Boutureira, T. Rodrigues, G. Jiménez-Osés, G. J . L. Bernardes
Angew. Chem. Int. Ed. 2017, 56, 243-247


2016

40. Antibody-drug conjugates: The missing link
T. Rodrigues, G. J. L. Bernardes
Nat. Chem. 2016, 8, 1088-1090

39. Unveiling (-)-englerin A as a L-type calcium channel modulator
T. Rodrigues*, F. Sieglitz, V. J. Somovilla, P. M. S. D. Cal, A. Galione, F. Corzana*, G. J. L. Bernardes*
Angew. Chem. Int. Ed. 2016, 55, 11077-11081

38. From complex natural products to simple synthetic mimetics by computational de novo design
L. Friedrich, T. Rodrigues, P. Schneider, G. Schneider
Angew. Chem. Int. Ed. 2016, 55, 6789-6792

37. Counting on natural products for drug design
T. Rodrigues, D. Reker, P. Schneider, G. Schneider
Nat. Chem. 2016, 8, 531-541

36. Natural product modulators of Transient Receptor Potential (TRP) channels as potential anti-cancer agents
T. Rodrigues, F. Sieglitz, G. J. B. Bernardes
Chem. Soc. Rev. 2016, 45, 6130-6137

35. Designing multi-target compound libraries with Gaussian process models
M. Bieler, M. Reutlinger, T. Rodrigues, P. Schneider, J. M. Kriegl, G. Schneider
Mol. Inf. 2016, 35, 192-198


2015

34. De novo fragment design for drug discovery and chemical biology
T. Rodrigues, D. Reker, M. Welin, M. Caldera, C. Brunner, G. Bagernet, P. Schneider, B. Walse, G. Schneider
Angew. Chem. Int. Ed. 2015, 54, 15079-15083

33. Revealing the macromolecular targets of fragment-like natural products
T. Rodrigues, D. Reker, J. Kunze, P. Schneider, G. Schneider
Angew. Chem. Int. Ed. 2015, 54, 10516-10520

32. Fragment-based de novo design reveals a small molecule inhibitor of Helicobacter pylori HtrA
A. M. Perna*, T. Rodrigues*, T. P. Schmidt, M. Böhm, K. Stutz, D. Reker, B. Pfeiffer, K.-H. Altmann, S. Backert, S. Wessler, G. Schneider
Angew. Chem. Int. Ed. 2015, 54, 10244-10248

31. Repurposing de novo designed entities reveals phosphodiesterase 3B and cathepsin L modulators
T. Rodrigues, Y.-C. Lin, M. Hartenfeller, S. Renner, Y. F. Lim, G. Schneider
Chem. Commun. 2015, 51, 7478-7481

30. Multidimensional de novo design reveals 5-HT2B receptor-selective ligands
T. Rodrigues, N. Hauser, D. Reker, M. Reutlinger, T. Wunderlin, J. Hamon, G. Koch, G. Schneider
Angew. Chem. Int. Ed. 2015, 54, 1551-1555


Prior to 2015

29. Revealing the macromolecular targets of complex natural products
D. Reker, A. M. Perna, T. Rodrigues, P. Schneider, M. Reutlinger, B. Mönch, A. Koeberle, C. Lamers, M. Gabler, H. Steinmetz, R. Müller, M. Schubert-Zsilavecz, O. Werz, G. Schneider
Nat. Chem. 2014, 6, 1072-1078

28. Coping with polypharmacology by computational medicinal chemistry
G. Schneider, D. Reker, T. Rodrigues, P. Schneider
Chimia 2014, 68, 648-653

27. Antiplasmodial drugs in the gas phase: A CID and DFT study of quinolon-4(1H)-imine derivatives
P. J. A. Madeira, A. R. F. Sitoe, D. Gonçalves, T. Rodrigues, R. C. Guedes, F. Lopes, R. Moreira, M. R. Bronze
J. Am. Soc. Mass Spectrom. 2014, 25, 1650-1661

26. Accessing new chemical entities using microfluidic technology
T. Rodrigues, P. Schneider, G. Schneider
Angew. Chem. Int. Ed. 2014, 53, 5750-5758

25. Identifying the macromolecular targets of de novo designed chemical entities through self-organizing map consensus
D. Reker, T. Rodrigues, P. Schneider, G. Schneider
Proc. Natl. Acad. Sci. USA 2014, 111, 4067-4072


24. Targeting dynamic pockets of HIV-1 protease by structure-based computational screening for allosteric inhibitors
J. Kunze, N. Todoroff, P. Schneider, T. Rodrigues, T. Geppert, F. Reisen, H. Schreuder, J. Saas, G. Hessler, K.-H. Baringhaus, G. Schneider
J. Chem. Inf. Model. 2014, 54, 987-991

23. Multi-objective molecular de novo design by fragment prioritization
M. Reutlinger, T. Rodrigues, P. Schneider, G. Schneider
Angew. Chem. Int. Ed. 2014, 53, 4244-4248

22. Combinatorial chemistry by ant colony optimization
J. A. Hiss, M. Reutlinger, C. P. Koch, A. M. Perna, P. Schneider, T. Rodrigues, S. Haller, G. Folkers, L. Weber, R. B. Baleeiro, P. Walden, P. Wrede, G. Schneider
Future Med. Chem. 2014, 6, 267-280

21. Combining on-chip synthesis of a focused combinatorial library with computational target prediction reveals imidazopyridine GPCR ligands
M. Reutlinger, T. Rodrigues, P. Schneider, G. Schneider
Angew. Chem. Int. Ed. 2014, 53, 582-585

20. Flashback forward: Reaction-driven de novo design of bioactive compounds
T. Rodrigues, G. Schneider
Synlett 2014, 25, 170-178

19. Flavones as isosteres of 4(1H)-quinolones: discovery of ligand efficient and dual stage antimalarial lead compounds
T. Rodrigues*, A. S. Ressurreição, F. P. da Cruz, I. S. Albuquerque, J. Gut, M. P. Carrasco, D. Gonçalves, R. C. Guedes, D. J. V. A. dos Santos, M. M. Mota, P. J. Rosenthal, R. Moreira, M. Prudêncio, F. Lopes
Eur. J. Med. Chem. 2013, 69, 872-880

18. Steering target selectivity and potency by fragment-based de novo drug design
T. Rodrigues, T. Kudoh, F. Roudnicky, Y. F. Lim, Y.-C. Lin, C. P. Koch, M. Seno, M. Detmar, G. Schneider
Angew. Chem. Int. Ed. 2013, 52, 10006-10009

17. Exploring the Molecular Basis of Qo bc1 Complex Inhibitors Activity to Find Novel Antimalarials Hits
M. P. Carrasco, J. Gut, T. Rodrigues, F. Lopes, P. J. Rosenthal, R. Moreira, D. J. V. A. dos Santos
Mol. Inf. 2013, 32, 659-670

16. Quinolin-4(1H)-imines are Potent Antiplasmodial Drugs Targeting the Liver Stage of Malaria
T. Rodrigues*, F. P. da Cruz, Maria J. Lafuente-Monasterio, D. Gonçalves, A. S. Ressurreição, A. R. Sitoe, M. R. Bronze, J. Gut, G. Schneider, M. M. Mota, P. J. Rosenthal, M. Prudêncio, F.-J. Gamo, F. Lopes, R. Moreira
J. Med. Chem. 2013, 56, 4811-4815

15. Chemically advanced template search (CATS) for scaffold-hopping and prospective target prediction for ‘orphan’ molecules
M. Reutlinger, C. P. Koch, D. Reker, N. Todoroff, P. Schneider, T. Rodrigues, G. Schneider
Mol. Inf. 2013, 32, 133-138

14. De novo design and optimization of Aurora A kinase inhibitors
T. Rodrigues, F. Roudnicky, K. P. Koch, T. Kudoh, D. Reker, M. Detmar, G. Schneider
Chem. Sci. 2013, 4, 1229-1233

13. Drugs by numbers: Reaction-driven de novo design of potent and selective anticancer leads
B. Spänkuch, S. Keppner, L. Lange, T. Rodrigues, H. Zettl, C. P. Koch, M. Reutlinger, M. Hartenfeller, P. Schneider, G. Schneider
Angew. Chem. Int. Ed. 2013, 52, 4676-4681

12. Significance estimation for sequence-based chemical similarity searching (PhAST) and application to Aurora A kinase inhibitors
V. Hähnke, N. Todoroff, T. Rodrigues, G. Schneider
Future Med. Chem. 2012, 4, 1897-1906

11. Drug screen targeted at Plasmodium liver stages identifies a potent multi-stage anti-malarial drug
F. P. da Cruz, C. Martin, K. Buchholz, M. J. Lafuente-Monasterio, T. Rodrigues, B. Sönnichsen, R. Moreira, F.-J. Gamo, M. Marti, M. M. Mota, M. Hannus, M. Prudêncio
J. Infect. Dis. 2012, 205, 1278-1286

10. Targeting the Liver Stage of Malaria Parasites: A Yet Unmet Goal
T. Rodrigues, M. Prudêncio, R. Moreira, M. M. Mota, F. Lopes
J. Med. Chem. 2012, 55, 995-1012

9. From virtual screening to bioactive compounds by visualizing and clustering of chemical space
A. Klenner, V. Hähnke, T. Geppert, P. Schneider, H. Zettl, S. Haller, T. Rodrigues, F. Reisen, B. Hoy, A. M. Schaible, O. Werz, S. Wessler, G. Schneider
Mol. Inf. 2012, 31, 21-26

8. Microwave-assisted Wittig reaction of semistabilized nitro-substituted benzyltriphenyl-phosphorous ylides with aldehydes in phase-transfer conditions
T. Rodrigues, F. Lopes, R. Moreira
Synth. Commun. 2012, 42, 747-755

7. Identification of new antimalarial leads by use of virtual screening against cytochrome bc1
T. Rodrigues, J. Gut, P. J. Rosenthal, P. M. O’Neill, G. A. Biagini, R. Moreira, F. Lopes, D. J. V. A. dos Santos, R. C. Guedes
Bioorg. Med. Chem. 2011, 19, 6302-6308

6. New hope in the fight against malaria?
T. Rodrigues*, R. Moreira, F. Lopes
Future Med. Chem. 2011, 3, 1-3

5. A quantum mechanical study of novel potential inhibitors of cytochrome bc1 as antimalarial compounds
T. Rodrigues, D. J. V. A. dos Santos, R. Moreira, F. Lopes, R. C. Guedes
Int. J. Quantum Chem. 2011, 111, 1196-1207

4. Inhibitors of the Mitochondrial Electron Transport Chain and de novo Pyrimidine Biosynthesis as Antimalarials: The Present Status
T. Rodrigues, F. Lopes, R. Moreira
Curr. Med. Chem. 2010, 17, 929-956

3. Design, synthesis and Structure Activity-Relationships of (1H-pyridin-4-ylidene)amines as potential antimalarials
T. Rodrigues, R. C. Guedes, D. J. V. A. dos Santos, M. Carrasco, J. Gut, P. J. Rosenthal, R. Moreira, F. Lopes
Bioorg. Med. Chem. Lett. 2009, 19, 3476-3480

2. Bis{(E)-3-[(diethylmethylammonio)methyl]-N-[3-(N,N-dimethylsulfamoyl)-1-methylpyridin-4-ylidene]-4-methoxyanilinium} tetraiodide pentahydrate
T. Rodrigues, R. Moreira, B. Dacunha-Marinho, F. Lopes
Acta Cryst. E 2009, E65, o283-o284

1. Unanticipated Acyloxymethylation of Sumatriptan Indole Nitrogen Atom and its Implications in Prodrug Design
T. Rodrigues, R. Moreira, R. C. Guedes, J. Iley, F. Lopes
Arch. Pharm. Chem. Life Sci. 2008, 341, 344-350