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Myc Transcription Factor Inhibitor Design: Integrating Atomic and Mesoscale with Semi-Supervised Generative Deep Learning Models

Award Number: F30GM147909
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: FELLOWSHIP/SCHOLARSHIP/STUDENT LOANS
PERIOD OF PERFORMANCE START DATE: 09/01/2022
PERIOD OF PERFORMANCE END DATE: 08/31/2027

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Myc Transcription Factor Inhibitor Design: Integrating Atomic and Mesoscale with Semi-Supervised Generative Deep Learning Models - C ABSTRACT Myc Transcription Factor Inhibitor Design: Integrating Atomic and Mesoscale with Semi-Supervised Gen- erative Deep Learning Models Inhibition of master regulators such as Myc have considerable interest due to the reversal of the oncogenic state evoked by their removal. Adding to the mystique is the technical challenge in targeting a protein which possesses large regions of disorder. Though widely considered “undruggable”, the library of hits that disrupt Myc function continuously grows. The chemical features of a hit are difﬁcult to deduce besides high molecular weight, aro- maticity, rigidity, and hydrophobicity. Understanding the more speciﬁc features of a protein-protein interaction (PPI) inhibitor is considerably difﬁcult. In order to circumvent answering this question, machine learning methods have been applied to expand the library of experimentally determined hits in hopes of ﬁnding an improved inhibitor nearby in chemical space. Recently, the natural application of generative deep learning techniques to this prob- lem have been reported. This proposal explains a protocol for a semi-supervised expansion of small molecules which inhibit various reactions in the Myc transactivation pathway. The PPI inhibitors from three publicly available databases make up the training set (n=9516) while the known Myc inhibitors are the test set (n=100). In order to surpass the effectiveness of the test set, all known Myc inhibitors are removed from the training set. A number of latent variables which sufﬁce to recreate the training set are solved. These variables represent the general struc- tural properties of PPI inhibitors, which may be associated with activities at various binding sites. The efﬁcient calculation of activities is crucial to obtaining good performance. Therefore, a well-tempered ensemble of target conﬁgurations is pre-calculated at the all-atom resolution. Additionally, in order to incorporate the population level behavior of multiple Myc molecules into inhibitor design, mesoscale coarse-grain simulations in various sol- vents which drive liquid-liquid phase separation are performed. To identify interactions which correlate with phase response, various points in coarse-grain phase space are converted to all-atom resolution, further reﬁned, and converted into contact maps. When evaluating a new lead, ensemble-based docking calculations are used, which calculate an average of averages of a ligand in different poses binding to different conformations randomly drawn from the ensembles. Reinforcement learning is applied to signiﬁcantly reduce the time spent docking batches of leads while maintaining conﬁdence in the result. Once new molecules are generated, these new leads are also optimized using absolute and relative free energy of binding methods. Ultimately, this study will test the limits of generative models to integrate data across multiple scales and develop inhibitors which evoke potent inhibition of intrinsically disordered proteins.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2025 ( Subtotal = $54,538 )
2025	2025	WAYNE STATE UNIVERSITY	5700 CASS AVE STE 4900	DETROIT	MI	48202	WAYNE	USA	Biomedical Research and Research Training	000	4	8/5/2025	NON-COMPETING CONTINUATION	$54,538
														Subtotal = $54,538

Issue Date FY: 2024 ( Subtotal = $47,979 )
2024	2024	WAYNE STATE UNIVERSITY	5700 CASS AVE STE 4900	DETROIT	MI	48202	WAYNE	USA	Biomedical Research and Research Training	000	3	8/29/2024	NON-COMPETING CONTINUATION	$47,979
														Subtotal = $47,979

Issue Date FY: 2023 ( Subtotal = $46,699 )
2023	2023	WAYNE STATE UNIVERSITY	5700 CASS AVE STE 4900	DETROIT	MI	48202	WAYNE	USA	Biomedical Research and Research Training	000	2	8/4/2023	NON-COMPETING CONTINUATION	$46,699
														Subtotal = $46,699

Issue Date FY: 2022 ( Subtotal = $45,757 )
2022	2022	WAYNE STATE UNIVERSITY	5057 WOODWARD STE 13001	DETROIT	MI	48202	WAYNE	USA	Biomedical Research and Research Training	001	1	9/1/2022	NEW	$0
2022	2022	WAYNE STATE UNIVERSITY	5057 WOODWARD STE 13001	DETROIT	MI	48202	WAYNE	USA	Biomedical Research and Research Training	000	1	9/1/2022	NEW	$45,757
														Subtotal = $45,757

Grand Total All Awards = $194,973

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Myc Transcription Factor Inhibitor Design: Integrating Atomic and Mesoscale with Semi-Supervised Generative Deep Learning Models

Award Number: F30GM147909

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: FELLOWSHIP/SCHOLARSHIP/STUDENT LOANS

PERIOD OF PERFORMANCE START DATE: 09/01/2022

PERIOD OF PERFORMANCE END DATE: 08/31/2027

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