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2. Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases.

Author

Koldenhof, Patrick, Bemelmans, Martijn P., Ghosh, Brahma, Damm‐Ganamet, Kelly L., van Vlijmen, Herman W. T., and Pande, Vineet

Abstract

Proteolysis Targeting Chimeras (PROTACs) are an emerging therapeutic modality and chemical biology tools for Targeted Protein Degradation (TPD). PROTACs contain a ligand targeting the protein of interest, a ligand recruiting an E3 ligase and a linker connecting these two ligands. There are over 600 E3 ligases known so far, but only a handful have been exploited for TPD applications. A key reason for this is the scarcity of ligands binding various E3 ligases and the paucity of structural data available, which complicates ligand design across the family. In this study, we aim to progress PROTAC discovery by proposing a shortlist of E3 ligases that can be prioritized for covalent targeting by performing systematic structural ligandability analysis on a chemoproteomic dataset of potentially reactive cysteines across hundreds of E3 ligases. One of the goals of this study is to apply AlphaFold (AF) models for ligandability evaluations, as for a vast majority of these ligases an experimental structure is not available in the protein data bank (PDB). Using a combination of pocket features, AF model quality and additional aspects, we propose a shortlist of E3 ligases and corresponding cysteines that can be prioritized to potentially discover covalent ligands and expand the PROTAC toolbox. [ABSTRACT FROM AUTHOR]

Published
2024
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3. Development of small molecule inhibitors of natural killer group 2D receptor (NKG2D)

Author

Wang, Jocelyn, primary, Nakafuku, Kohki M., additional, Ziff, Jeannie, additional, Gelin, Christine F., additional, Gholami, Hadi, additional, Thompson, Aaron A., additional, Karpowich, Nathan K., additional, Limon, Luis, additional, Coate, Heather R., additional, Damm-Ganamet, Kelly L., additional, Shih, Amy Y., additional, Grant, Joanna C., additional, Côte, Marjorie, additional, Mak, Puiying A., additional, Pascual, Heather A., additional, Rives, Marie-Laure, additional, Edwards, James P., additional, Venable, Jennifer D., additional, Venkatesan, Hariharan, additional, Shi, Zhicai, additional, Allen, Samantha J., additional, Sharma, Sujata, additional, Kung, Pei-Pei, additional, and Shireman, Brock T., additional

Published
2023
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4. Identification of small-molecule protein–protein interaction inhibitors for NKG2D

Author

Thompson, Aaron A., primary, Harbut, Michael B., additional, Kung, Pei-Pei, additional, Karpowich, Nathan K., additional, Branson, Jeffrey D., additional, Grant, Joanna C., additional, Hagan, Deborah, additional, Pascual, Heather A., additional, Bai, Guoyun, additional, Zavareh, Reza Beheshti, additional, Coate, Heather R., additional, Collins, Bernard C., additional, Côte, Marjorie, additional, Gelin, Christine F., additional, Damm-Ganamet, Kelly L., additional, Gholami, Hadi, additional, Huff, Adam R., additional, Limon, Luis, additional, Lumb, Kevin J., additional, Mak, Puiying A., additional, Nakafuku, Kohki M., additional, Price, Edmund V., additional, Shih, Amy Y., additional, Tootoonchi, Mandana, additional, Vellore, Nadeem A., additional, Wang, Jocelyn, additional, Wei, Na, additional, Ziff, Jeannie, additional, Berger, Scott B., additional, Edwards, James P., additional, Gardet, Agnès, additional, Sun, Siquan, additional, Towne, Jennifer E., additional, Venable, Jennifer D., additional, Shi, Zhicai, additional, Venkatesan, Hariharan, additional, Rives, Marie-Laure, additional, Sharma, Sujata, additional, Shireman, Brock T., additional, and Allen, Samantha J., additional

Published
2023
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7. Accelerating Lead Identification by High Throughput Virtual Screening: Prospective Case Studies from the Pharmaceutical Industry

Author

Damm-Ganamet, Kelly L., primary, Arora, Nidhi, additional, Becart, Stephane, additional, Edwards, James P., additional, Lebsack, Alec D., additional, McAllister, Heather M., additional, Nelen, Marina I., additional, Rao, Navin L., additional, Westover, Lori, additional, Wiener, John J. M., additional, and Mirzadegan, Taraneh, additional

Published
2019
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9. CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma

Author

Carlson, Heather A., primary, Smith, Richard D., additional, Damm-Ganamet, Kelly L., additional, Stuckey, Jeanne A., additional, Ahmed, Aqeel, additional, Convery, Maire A., additional, Somers, Donald O., additional, Kranz, Michael, additional, Elkins, Patricia A., additional, Cui, Guanglei, additional, Peishoff, Catherine E., additional, Lambert, Millard H., additional, and Dunbar, James B., additional

Published
2016
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10. A Prospective Virtual Screening Study: Enriching Hit Rates and Designing Focus Libraries To Find Inhibitors of PI3Kδ and PI3Kγ

Author

Damm-Ganamet, Kelly L., primary, Bembenek, Scott D., additional, Venable, Jennifer W., additional, Castro, Glenda G., additional, Mangelschots, Lieve, additional, Peeters, Daniëlle C. G., additional, Mcallister, Heather M., additional, Edwards, James P., additional, Disepio, Daniel, additional, and Mirzadegan, Taraneh, additional

Published
2016
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11. Overcoming Sequence Misalignments with Weighted Structural Superposition

Author

Khazanov, Nickolay A., Damm-Ganamet, Kelly L., Quang, Daniel X., and Carlson, Heather A.

Subjects
Models, Molecular, Sequence Homology, Amino Acid, Protein Conformation, Sequence Analysis, Protein, Structural Homology, Protein, Molecular Sequence Data, Proteins, Amino Acid Sequence, Databases, Protein, Sequence Alignment, Article, Algorithms
Abstract

An appropriate structural superposition identifies similarities and differences between homologous proteins that are not evident from sequence alignments alone. We have coupled our Gaussian-weighted RMSD (wRMSD) tool with a sequence aligner and seed extension (SE) algorithm to create a robust technique for overlaying structures and aligning sequences of homologous proteins (HwRMSD). HwRMSD overcomes errors in the initial sequence alignment that would normally propagate into a standard RMSD overlay. SE can generate a corrected sequence alignment from the improved structural superposition obtained by wRMSD. HwRMSD's robust performance and its superiority over standard RMSD are demonstrated over a range of homologous proteins. Its better overlay results in corrected sequence alignments with good agreement to HOMSTRAD. Finally, HwRMSD is compared to established structural alignment methods: FATCAT, secondary-structure matching, combinatorial extension, and Dalilite. Most methods are comparable at placing residue pairs within 2 Å, but HwRMSD places many more residue pairs within 1 Å, providing a clear advantage. Such high accuracy is essential in drug design, where small distances can have a large impact on computational predictions. This level of accuracy is also needed to correct sequence alignments in an automated fashion, especially for omics-scale analysis. HwRMSD can align homologs with low-sequence identity and large conformational differences, cases where both sequence-based and structural-based methods may fail. The HwRMSD pipeline overcomes the dependency of structural overlays on initial sequence pairing and removes the need to determine the best sequence-alignment method, substitution matrix, and gap parameters for each unique pair of homologs.

Published
2012

12. CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge

Author

Smith, Richard D., primary, Damm-Ganamet, Kelly L., additional, Dunbar, James B., additional, Ahmed, Aqeel, additional, Chinnaswamy, Krishnapriya, additional, Delproposto, James E., additional, Kubish, Ginger M., additional, Tinberg, Christine E., additional, Khare, Sagar D., additional, Dou, Jiayi, additional, Doyle, Lindsey, additional, Stuckey, Jeanne A., additional, Baker, David, additional, and Carlson, Heather A., additional

Published
2015
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14. CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys

Author

Dunbar, James B., primary, Smith, Richard D., additional, Damm-Ganamet, Kelly L., additional, Ahmed, Aqeel, additional, Esposito, Emilio Xavier, additional, Delproposto, James, additional, Chinnaswamy, Krishnapriya, additional, Kang, You-Na, additional, Kubish, Ginger, additional, Gestwicki, Jason E., additional, Stuckey, Jeanne A., additional, and Carlson, Heather A., additional

Published
2013
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