1
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Rao SPS, Gould MK, Noeske J, Saldivia M, Jumani RS, Ng PS, René O, Chen YL, Kaiser M, Ritchie R, Francisco AF, Johnson N, Patra D, Cheung H, Deniston C, Schenk AD, Cortopassi WA, Schmidt RS, Wiedemar N, Thomas B, Palkar R, Ghafar NA, Manoharan V, Luu C, Gable JE, Wan KF, Myburgh E, Mottram JC, Barnes W, Walker J, Wartchow C, Aziz N, Osborne C, Wagner J, Sarko C, Kelly JM, Manjunatha UH, Mäser P, Jiricek J, Lakshminarayana SB, Barrett MP, Diagana TT. Cyanotriazoles are selective topoisomerase II poisons that rapidly cure trypanosome infections. Science 2023; 380:1349-1356. [PMID: 37384702 DOI: 10.1126/science.adh0614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/24/2023] [Indexed: 07/01/2023]
Abstract
Millions who live in Latin America and sub-Saharan Africa are at risk of trypanosomatid infections, which cause Chagas disease and human African trypanosomiasis (HAT). Improved HAT treatments are available, but Chagas disease therapies rely on two nitroheterocycles, which suffer from lengthy drug regimens and safety concerns that cause frequent treatment discontinuation. We performed phenotypic screening against trypanosomes and identified a class of cyanotriazoles (CTs) with potent trypanocidal activity both in vitro and in mouse models of Chagas disease and HAT. Cryo-electron microscopy approaches confirmed that CT compounds acted through selective, irreversible inhibition of trypanosomal topoisomerase II by stabilizing double-stranded DNA:enzyme cleavage complexes. These findings suggest a potential approach toward successful therapeutics for the treatment of Chagas disease.
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Affiliation(s)
- Srinivasa P S Rao
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Matthew K Gould
- College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jonas Noeske
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Manuel Saldivia
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Rajiv S Jumani
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Pearly S Ng
- Novartis Institute for Tropical Diseases, Singapore
| | - Olivier René
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Yen-Liang Chen
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Ryan Ritchie
- College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | - Nila Johnson
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
| | - Debjani Patra
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Harry Cheung
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Colin Deniston
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | | | | | - Remo S Schmidt
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Natalie Wiedemar
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Bryanna Thomas
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Rima Palkar
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
| | | | | | - Catherine Luu
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Jonathan E Gable
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Kah Fei Wan
- Novartis Institute for Tropical Diseases, Singapore
| | - Elmarie Myburgh
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | - Jeremy C Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Whitney Barnes
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - John Walker
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Charles Wartchow
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Natasha Aziz
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Colin Osborne
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Juergen Wagner
- Novartis Institute for Tropical Diseases, Singapore
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Christopher Sarko
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - John M Kelly
- London School of Hygiene and Tropical Medicine, London, UK
| | - Ujjini H Manjunatha
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Jan Jiricek
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Suresh B Lakshminarayana
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
| | - Michael P Barrett
- College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Thierry T Diagana
- Novartis Institute for Tropical Diseases, Emeryville, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
- Novartis Institute for Tropical Diseases, Singapore
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2
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Smithers L, Degtjarik O, Weichert D, Huang CY, Boland C, Bowen K, Oluwole A, Lutomski C, Robinson CV, Scanlan EM, Wang M, Olieric V, Shalev-Benami M, Caffrey M. Structure snapshots reveal the mechanism of a bacterial membrane lipoprotein N-acyltransferase. SCIENCE ADVANCES 2023; 9:eadf5799. [PMID: 37390210 PMCID: PMC10313180 DOI: 10.1126/sciadv.adf5799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/26/2023] [Indexed: 07/02/2023]
Abstract
Bacterial lipoproteins (BLPs) decorate the surface of membranes in the cell envelope. They function in membrane assembly and stability, as enzymes, and in transport. The final enzyme in the BLP synthesis pathway is the apolipoprotein N-acyltransferase, Lnt, which is proposed to act by a ping-pong mechanism. Here, we use x-ray crystallography and cryo-electron microscopy to chart the structural changes undergone during the progress of the enzyme through the reaction. We identify a single active site that has evolved to bind, individually and sequentially, substrates that satisfy structural and chemical criteria to position reactive parts next to the catalytic triad for reaction. This study validates the ping-pong mechanism, explains the molecular bases for Lnt's substrate promiscuity, and should facilitate the design of antibiotics with minimal off-target effects.
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Affiliation(s)
- Luke Smithers
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Oksana Degtjarik
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dietmar Weichert
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Chia-Ying Huang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Coilín Boland
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Katherine Bowen
- School of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Abraham Oluwole
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Corinne Lutomski
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Eoin M. Scanlan
- School of Chemistry, Trinity College Dublin, Dublin D02 R590, Ireland
| | - Meitian Wang
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Vincent Olieric
- Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Moran Shalev-Benami
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Martin Caffrey
- School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin D02 R590, Ireland
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3
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Chenthamarakshan V, Hoffman SC, Owen CD, Lukacik P, Strain-Damerell C, Fearon D, Malla TR, Tumber A, Schofield CJ, Duyvesteyn HME, Dejnirattisai W, Carrique L, Walter TS, Screaton GR, Matviiuk T, Mojsilovic A, Crain J, Walsh MA, Stuart DI, Das P. Accelerating drug target inhibitor discovery with a deep generative foundation model. SCIENCE ADVANCES 2023; 9:eadg7865. [PMID: 37343087 DOI: 10.1126/sciadv.adg7865] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/17/2023] [Indexed: 06/23/2023]
Abstract
Inhibitor discovery for emerging drug-target proteins is challenging, especially when target structure or active molecules are unknown. Here, we experimentally validate the broad utility of a deep generative framework trained at-scale on protein sequences, small molecules, and their mutual interactions-unbiased toward any specific target. We performed a protein sequence-conditioned sampling on the generative foundation model to design small-molecule inhibitors for two dissimilar targets: the spike protein receptor-binding domain (RBD) and the main protease from SARS-CoV-2. Despite using only the target sequence information during the model inference, micromolar-level inhibition was observed in vitro for two candidates out of four synthesized for each target. The most potent spike RBD inhibitor exhibited activity against several variants in live virus neutralization assays. These results establish that a single, broadly deployable generative foundation model for accelerated inhibitor discovery is effective and efficient, even in the absence of target structure or binder information.
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Affiliation(s)
| | - Samuel C Hoffman
- IBM Research, Thomas J. Watson Research Center, Yorktown Heights, New York, NY, USA
| | - C David Owen
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, UK
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, UK
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, UK
| | - Tika R Malla
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, UK
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Loic Carrique
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Thomas S Walter
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | | | | | - Jason Crain
- IBM Research Europe, Hartree Centre, Daresbury WA4 4AD, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, UK
| | - David I Stuart
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Payel Das
- IBM Research, Thomas J. Watson Research Center, Yorktown Heights, New York, NY, USA
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5
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Perkins A, Gretes MC, Nelson KJ, Poole LB, Karplus PA. Mapping the active site helix-to-strand conversion of CxxxxC peroxiredoxin Q enzymes. Biochemistry 2012; 51:7638-50. [PMID: 22928725 DOI: 10.1021/bi301017s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peroxiredoxins (Prx) make up a family of enzymes that reduce peroxides using a peroxidatic cysteine residue; among these, members of the PrxQ subfamily are proposed to be the most ancestral-like yet are among the least characterized. In many PrxQ enzymes, a second "resolving" cysteine is located five residues downstream from the peroxidatic Cys, and these residues form a disulfide during the catalytic cycle. Here, we describe three hyperthermophilic PrxQ crystal structures originally determined by the RIKEN structural genomics group. We reprocessed the diffraction data and conducted further refinement to yield models with R(free) values lowered by 2.3-7.2% and resolution extended by 0.2-0.3 Å, making one, at 1.4 Å, one of the best resolved peroxiredoxins to date. Comparisons of two matched thiol and disulfide forms reveal that the active site conformational change required for disulfide formation involves a transition of ~20 residues from a pair of α-helices to a β-hairpin and 3(10)-helix. Each conformation has ~10 residues with a high level of disorder providing slack that allows the dramatic shift, and the two conformations are anchored to the protein core by distinct nonpolar side chains that fill three hydrophobic pockets. Sequence conservation patterns confirm the importance of these and a few additional residues for function. From a broader perspective, this study raises the provocative question of how to make use of the valuable information in the Protein Data Bank generated by structural genomics projects but not described in the literature, perhaps remaining unrecognized and certainly underutilized.
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Affiliation(s)
- Arden Perkins
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
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