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Koscher BA, Canty RB, McDonald MA, Greenman KP, McGill CJ, Bilodeau CL, Jin W, Wu H, Vermeire FH, Jin B, Hart T, Kulesza T, Li SC, Jaakkola TS, Barzilay R, Gómez-Bombarelli R, Green WH, Jensen KF. Autonomous, multiproperty-driven molecular discovery: From predictions to measurements and back. Science 2023; 382:eadi1407. [PMID: 38127734 DOI: 10.1126/science.adi1407] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023]
Abstract
A closed-loop, autonomous molecular discovery platform driven by integrated machine learning tools was developed to accelerate the design of molecules with desired properties. We demonstrated two case studies on dye-like molecules, targeting absorption wavelength, lipophilicity, and photooxidative stability. In the first study, the platform experimentally realized 294 unreported molecules across three automatic iterations of molecular design-make-test-analyze cycles while exploring the structure-function space of four rarely reported scaffolds. In each iteration, the property prediction models that guided exploration learned the structure-property space of diverse scaffold derivatives, which were realized with multistep syntheses and a variety of reactions. The second study exploited property models trained on the explored chemical space and previously reported molecules to discover nine top-performing molecules within a lightly explored structure-property space.
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Affiliation(s)
- Brent A Koscher
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Richard B Canty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew A McDonald
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kevin P Greenman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Charles J McGill
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Camille L Bilodeau
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wengong Jin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Haoyang Wu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Florence H Vermeire
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brooke Jin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Travis Hart
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Timothy Kulesza
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shih-Cheng Li
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tommi S Jaakkola
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Regina Barzilay
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rafael Gómez-Bombarelli
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - William H Green
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Klavs F Jensen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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2
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Sutanto F, Shaabani S, Oerlemans R, Eris D, Patil P, Hadian M, Wang M, Sharpe ME, Groves MR, Dömling A. Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification. Angew Chem Int Ed Engl 2021; 60:18231-18239. [PMID: 34097796 PMCID: PMC8456925 DOI: 10.1002/anie.202105584] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/31/2021] [Indexed: 12/24/2022]
Abstract
Protein crystallography (PX) is widely used to drive advanced stages of drug optimization or to discover medicinal chemistry starting points by fragment soaking. However, recent progress in PX could allow for a more integrated role into early drug discovery. Here, we demonstrate for the first time the interplay of high throughput synthesis and high throughput PX. We describe a practical multicomponent reaction approach to acrylamides and -esters from diverse building blocks suitable for mmol scale synthesis on 96-well format and on a high-throughput nanoscale format in a highly automated fashion. High-throughput PX of our libraries efficiently yielded potent covalent inhibitors of the main protease of the COVID-19 causing agent, SARS-CoV-2. Our results demonstrate, that the marriage of in situ HT synthesis of (covalent) libraires and HT PX has the potential to accelerate hit finding and to provide meaningful strategies for medicinal chemistry projects.
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Affiliation(s)
- Fandi Sutanto
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Shabnam Shaabani
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Rick Oerlemans
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Deniz Eris
- Photon Science DivisionPaul Scherrer InstituteSwitzerland
| | - Pravin Patil
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Mojgan Hadian
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Meitian Wang
- Photon Science DivisionPaul Scherrer InstituteSwitzerland
| | | | - Matthew R. Groves
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Alexander Dömling
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
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3
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Sutanto F, Shaabani S, Oerlemans R, Eris D, Patil P, Hadian M, Wang M, Sharpe ME, Groves MR, Dömling A. Combining High‐Throughput Synthesis and High‐Throughput Protein Crystallography for Accelerated Hit Identification. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Fandi Sutanto
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Shabnam Shaabani
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Rick Oerlemans
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Deniz Eris
- Photon Science Division Paul Scherrer Institute Switzerland
| | - Pravin Patil
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Mojgan Hadian
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Meitian Wang
- Photon Science Division Paul Scherrer Institute Switzerland
| | | | - Matthew R. Groves
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Alexander Dömling
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
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