1
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Lou J, Zhou Q, Lyu X, Cen X, Liu C, Yan Z, Li Y, Tang H, Liu Q, Ding J, Lu Y, Huang H, Xie H, Zhao Y. Discovery of a Covalent Inhibitor That Overcame Resistance to Venetoclax in AML Cells Overexpressing BFL-1. J Med Chem 2024. [PMID: 38913996 DOI: 10.1021/acs.jmedchem.4c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Clinical and biological studies have shown that overexpression of BFL-1 is one contributing factor to venetoclax resistance. The resistance might be overcome by a potent BFL-1 inhibitor, but such an inhibitor is rare. In this study, we show that 56, featuring an acrylamide moiety, inhibited the BFL-1/BID interaction with a Ki value of 105 nM. More interestingly, 56 formed an irreversible conjugation adduct at the C55 residue of BFL-1. 56 was a selective BFL-1 inhibitor, and its MCL-1 binding affinity was 10-fold weaker, while it did not bind BCL-2 and BCL-xL. Mechanistic studies showed that 56 overcame venetoclax resistance in isogenic AML cell lines MOLM-13-OE and MV4-11-OE, which both overexpressed BFL-1. More importantly, 56 and venetoclax combination promoted stronger apoptosis induction than either single agent. Collectively, our data show that 56 overcame resistance to venetoclax in AML cells overexpressing BFL-1. These attributes make 56 a promising candidate for future optimization.
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Affiliation(s)
- Jianfeng Lou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Qianqian Zhou
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, PR China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xilin Lyu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
| | - Xinyi Cen
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chen Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ziqin Yan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
| | - Yan Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
| | - Haotian Tang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Qiupei Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
| | - Jian Ding
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, PR China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Ye Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - He Huang
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hua Xie
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, PR China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Yujun Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
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2
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Gupta SRR, Mittal P, Kundu B, Singh A, Singh IK. Silibinin: an inhibitor for a high-expressed BCL-2A1/BFL1 protein, linked with poor prognosis in breast cancer. J Biomol Struct Dyn 2023:1-11. [PMID: 37837418 DOI: 10.1080/07391102.2023.2268176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
Abstract
Breast cancer (BC) accounts for 30% of all diagnosed cases of cancer in women and remains a leading cause of cancer-related deaths among women worldwide. The current study looks for a protein from the anti-apoptotic/pro-survival BCL-2 family whose overexpression reduces survivability in BC patients and a potential inhibitor for the protein. We found BCL-2A1/BFL1 protein with high expression linked to low survivability in BC. The protein shows prognosis in 8 out of 29 categories, whereas no other family member manifests this property. Out of 7379 compounds, three small molecules (CHEMBL9509, CHEMBL2104550 and CHEMBL3545011) form an H-bond with BCL-2A1/BFL1 protein's unique residue Cys55. Of the three small molecules, we found CHEMBL9509 (Silibinin) to be a potent inhibitor. The compound forms a stable H-bond with the residue Cys55 with the lowest binding energy compared to the other two compounds. It remains stable in the BH3 binding region for more than 100 ns, whereas the other two detach from the region. Additionally, the compound is found to be better than Venetoclax and Nematoclax. We firmly believe in the compound CHEMBL9509 potency to halt BC's progression by inhibiting the BCL-2A1/BFL1 protein, increasing patients' survivability.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shradheya R R Gupta
- Molecular Biology Research Laboratory, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Pooja Mittal
- Molecular Biology Research Laboratory, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
- Norris Comprehensive Cancer Center, Division of Medical Oncology, University of Southern California, Los Angeles, USA
| | - Bishwajit Kundu
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, New Delhi, India
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi (South Campus), New Delhi, India
| | - Indrakant K Singh
- Molecular Biology Research Laboratory, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
- Norris Comprehensive Cancer Center, Division of Medical Oncology, University of Southern California, Los Angeles, USA
- Institute of Eminence, Delhi School of Public Health, University of Delhi, Delhi, India
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3
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Aguilar F, Yu S, Grant RA, Swanson S, Ghose D, Su BG, Sarosiek KA, Keating AE. Peptides from human BNIP5 and PXT1 and non-native binders of pro-apoptotic BAK can directly activate or inhibit BAK-mediated membrane permeabilization. Structure 2023; 31:265-281.e7. [PMID: 36706751 PMCID: PMC9992319 DOI: 10.1016/j.str.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/24/2022] [Accepted: 01/02/2023] [Indexed: 01/27/2023]
Abstract
Apoptosis is important for development and tissue homeostasis, and its dysregulation can lead to diseases, including cancer. As an apoptotic effector, BAK undergoes conformational changes that promote mitochondrial outer membrane disruption, leading to cell death. This is termed "activation" and can be induced by peptides from the human proteins BID, BIM, and PUMA. To identify additional peptides that can regulate BAK, we used computational protein design, yeast surface display screening, and structure-based energy scoring to identify 10 diverse new binders. We discovered peptides from the human proteins BNIP5 and PXT1 and three non-native peptides that activate BAK in liposome assays and induce cytochrome c release from mitochondria. Crystal structures and binding studies reveal a high degree of similarity among peptide activators and inhibitors, ruling out a simple function-determining property. Our results shed light on the vast peptide sequence space that can regulate BAK function and will guide the design of BAK-modulating tools and therapeutics.
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Affiliation(s)
- Fiona Aguilar
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stacey Yu
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Program in Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA; John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sebastian Swanson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dia Ghose
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bonnie G Su
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kristopher A Sarosiek
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Program in Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA; John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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4
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Zhang P, Walko M, Wilson AJ. Rational design of Harakiri (HRK)-derived constrained peptides as BCL-x L inhibitors. Chem Commun (Camb) 2023; 59:1697-1700. [PMID: 36692261 PMCID: PMC9904277 DOI: 10.1039/d2cc06029a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Using the HRK BH3 domain, sequence hybridization and in silico methods we show dibromomaleimide staple scanning can be used to inform the design of BCL-xL selective peptidomimetic ligands. These HRK-inspired reagents may serve as starting points for the discovery of therapeutics to target BCL-xL-overexpressed cancers.
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Affiliation(s)
- Peiyu Zhang
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Martin Walko
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Andrew J. Wilson
- School of Chemistry, University of Leeds, Woodhouse LaneLeedsLS2 9JTUK,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse LaneLeedsLS2 9JTUK
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5
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Ground type-I collagen—a focused study on its fibrillogenesis behavior and bioactivity in vitro. Macromol Res 2023. [DOI: 10.1007/s13233-022-00108-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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6
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Li AJ, Lu M, Desta I, Sundar V, Grigoryan G, Keating AE. Neural network-derived Potts models for structure-based protein design using backbone atomic coordinates and tertiary motifs. Protein Sci 2023; 32:e4554. [PMID: 36564857 PMCID: PMC9854172 DOI: 10.1002/pro.4554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/15/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
Abstract
Designing novel proteins to perform desired functions, such as binding or catalysis, is a major goal in synthetic biology. A variety of computational approaches can aid in this task. An energy-based framework rooted in the sequence-structure statistics of tertiary motifs (TERMs) can be used for sequence design on predefined backbones. Neural network models that use backbone coordinate-derived features provide another way to design new proteins. In this work, we combine the two methods to make neural structure-based models more suitable for protein design. Specifically, we supplement backbone-coordinate features with TERM-derived data, as inputs, and we generate energy functions as outputs. We present two architectures that generate Potts models over the sequence space: TERMinator, which uses both TERM-based and coordinate-based information, and COORDinator, which uses only coordinate-based information. Using these two models, we demonstrate that TERMs can be utilized to improve native sequence recovery performance of neural models. Furthermore, we demonstrate that sequences designed by TERMinator are predicted to fold to their target structures by AlphaFold. Finally, we show that both TERMinator and COORDinator learn notions of energetics, and these methods can be fine-tuned on experimental data to improve predictions. Our results suggest that using TERM-based and coordinate-based features together may be beneficial for protein design and that structure-based neural models that produce Potts energy tables have utility for flexible applications in protein science.
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Affiliation(s)
- Alex J. Li
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Mindren Lu
- Department of Electrical Engineering and Computer ScienceMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Israel Desta
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Vikram Sundar
- Computational and Systems Biology ProgramMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Gevorg Grigoryan
- Department of Computer ScienceDartmouth CollegeHanoverNew HampshireUSA
| | - Amy E. Keating
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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7
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Aguilar Rangel M, Bedwell A, Costanzi E, Taylor RJ, Russo R, Bernardes GJL, Ricagno S, Frydman J, Vendruscolo M, Sormanni P. Fragment-based computational design of antibodies targeting structured epitopes. SCIENCE ADVANCES 2022; 8:eabp9540. [PMID: 36367941 PMCID: PMC9651861 DOI: 10.1126/sciadv.abp9540] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
De novo design methods hold the promise of reducing the time and cost of antibody discovery while enabling the facile and precise targeting of predetermined epitopes. Here, we describe a fragment-based method for the combinatorial design of antibody binding loops and their grafting onto antibody scaffolds. We designed and tested six single-domain antibodies targeting different epitopes on three antigens, including the receptor-binding domain of the SARS-CoV-2 spike protein. Biophysical characterization showed that all designs are stable and bind their intended targets with affinities in the nanomolar range without in vitro affinity maturation. We further discuss how a high-resolution input antigen structure is not required, as similar predictions are obtained when the input is a crystal structure or a computer-generated model. This computational procedure, which readily runs on a laptop, provides a starting point for the rapid generation of lead antibodies binding to preselected epitopes.
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Affiliation(s)
- Mauricio Aguilar Rangel
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Alice Bedwell
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Elisa Costanzi
- Department of Bioscience, Università degli Studi di Milano, Milano 20133, Italy
| | - Ross J. Taylor
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Rosaria Russo
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milano 20122, Italy
| | - Gonçalo J. L. Bernardes
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Stefano Ricagno
- Department of Bioscience, Università degli Studi di Milano, Milano 20133, Italy
- Institute of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, Milan 20097, Italy
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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8
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Last but not least: BFL-1 as an emerging target for anti-cancer therapies. Biochem Soc Trans 2022; 50:1119-1128. [PMID: 35900226 PMCID: PMC9444066 DOI: 10.1042/bst20220153] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/17/2022]
Abstract
BFL-1 is an understudied pro-survival BCL-2 protein. The expression of BFL-1 is reported in many cancers, but it is yet to be clarified whether high transcript expression also always correlates with a pro-survival function. However, recent applications of BH3-mimetics for the treatment of blood cancers identified BFL-1 as a potential resistance factor in this type of cancer. Hence, understanding the role of BFL-1 in human cancers and how its up-regulation leads to therapy resistance has become an area of great clinical relevance. In addition, deletion of the murine homologue of BFL-1, called A1, in mice showed only minimal impacts on the well-being of these animals, suggesting drugs targeting BFL-1 would exhibit limited on-target toxicities. BFL-1 therefore represents a good clinical cancer target. Currently, no effective BFL-1 inhibitors exist, which is likely due to the underappreciation of BFL-1 as a potential target in the clinic and lack of understanding of the BFL-1 protein. In this review, the roles of BFL-1 in the development of different types of cancers and drug resistant mechanisms are discussed and some recent advances in the generation of BFL-1 inhibitors highlighted.
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9
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Swanson S, Sivaraman V, Grigoryan G, Keating AE. Tertiary motifs as building blocks for the design of protein‐binding peptides. Protein Sci 2022; 31:e4322. [PMID: 35634780 PMCID: PMC9088223 DOI: 10.1002/pro.4322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Sebastian Swanson
- Department of Biology Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Venkatesh Sivaraman
- Department of Biology Massachusetts Institute of Technology Cambridge Massachusetts USA
| | - Gevorg Grigoryan
- Department of Computer Science Dartmouth College Hanover New Hampshire USA
| | - Amy E. Keating
- Department of Biology Massachusetts Institute of Technology Cambridge Massachusetts USA
- Department of Biological Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA
- Koch Center for Integrative Cancer Research Massachusetts Institute of Technology Cambridge Massachusetts USA
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10
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Gupta S, Azadvari N, Hosseinzadeh P. Design of Protein Segments and Peptides for Binding to Protein Targets. BIODESIGN RESEARCH 2022; 2022:9783197. [PMID: 37850124 PMCID: PMC10521657 DOI: 10.34133/2022/9783197] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/16/2022] [Indexed: 10/19/2023] Open
Abstract
Recent years have witnessed a rise in methods for accurate prediction of structure and design of novel functional proteins. Design of functional protein fragments and peptides occupy a small, albeit unique, space within the general field of protein design. While the smaller size of these peptides allows for more exhaustive computational methods, flexibility in their structure and sparsity of data compared to proteins, as well as presence of noncanonical building blocks, add additional challenges to their design. This review summarizes the current advances in the design of protein fragments and peptides for binding to targets and discusses the challenges in the field, with an eye toward future directions.
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Affiliation(s)
- Suchetana Gupta
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Noora Azadvari
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Parisa Hosseinzadeh
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
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11
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Delaunay M, Ha-Duong T. Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2405:205-230. [PMID: 35298816 DOI: 10.1007/978-1-0716-1855-4_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein-protein interactions play crucial and subtle roles in many biological processes and modifications of their fine mechanisms generally result in severe diseases. Peptide derivatives are very promising therapeutic agents for modulating protein-protein associations with sizes and specificities between those of small compounds and antibodies. For the same reasons, rational design of peptide-based inhibitors naturally borrows and combines computational methods from both protein-ligand and protein-protein research fields. In this chapter, we aim to provide an overview of computational tools and approaches used for identifying and optimizing peptides that target protein-protein interfaces with high affinity and specificity. We hope that this review will help to implement appropriate in silico strategies for peptide-based drug design that builds on available information for the systems of interest.
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Affiliation(s)
| | - Tâp Ha-Duong
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France.
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12
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Hetherington K, Dutt S, Ibarra AA, Cawood EE, Hobor F, Woolfson DN, Edwards TA, Nelson A, Sessions RB, Wilson AJ. Towards optimizing peptide-based inhibitors of protein-protein interactions: predictive saturation variation scanning (PreSaVS). RSC Chem Biol 2021; 2:1474-1478. [PMID: 34704051 PMCID: PMC8495968 DOI: 10.1039/d1cb00137j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 07/30/2021] [Indexed: 12/21/2022] Open
Abstract
A simple-to-implement and experimentally validated computational workflow for sequence modification of peptide inhibitors of protein–protein interactions (PPIs) is described. An experimentally validated approach for in silico modification of peptide based protein–protein interaction inhibitors is described.![]()
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Affiliation(s)
- Kristina Hetherington
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Som Dutt
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Amaurys A Ibarra
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
| | - Emma E Cawood
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Fruzsina Hobor
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Derek N Woolfson
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK .,School of Chemistry, University of Bristol, Cantock's Close Bristol BS8 1TS UK.,BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Adam Nelson
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK .,BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK .,School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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13
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Woolfson DN. A Brief History of De Novo Protein Design: Minimal, Rational, and Computational. J Mol Biol 2021; 433:167160. [PMID: 34298061 DOI: 10.1016/j.jmb.2021.167160] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 12/26/2022]
Abstract
Protein design has come of age, but how will it mature? In the 1980s and the 1990s, the primary motivation for de novo protein design was to test our understanding of the informational aspect of the protein-folding problem; i.e., how does protein sequence determine protein structure and function? This necessitated minimal and rational design approaches whereby the placement of each residue in a design was reasoned using chemical principles and/or biochemical knowledge. At that time, though with some notable exceptions, the use of computers to aid design was not widespread. Over the past two decades, the tables have turned and computational protein design is firmly established. Here, I illustrate this progress through a timeline of de novo protein structures that have been solved to atomic resolution and deposited in the Protein Data Bank. From this, it is clear that the impact of rational and computational design has been considerable: More-complex and more-sophisticated designs are being targeted with many being resolved to atomic resolution. Furthermore, our ability to generate and manipulate synthetic proteins has advanced to a point where they are providing realistic alternatives to natural protein functions for applications both in vitro and in cells. Also, and increasingly, computational protein design is becoming accessible to non-specialists. This all begs the questions: Is there still a place for minimal and rational design approaches? And, what challenges lie ahead for the burgeoning field of de novo protein design as a whole?
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK; Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
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14
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Frappier V, Keating AE. Data-driven computational protein design. Curr Opin Struct Biol 2021; 69:63-69. [PMID: 33910104 DOI: 10.1016/j.sbi.2021.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 01/28/2023]
Abstract
Computational protein design can generate proteins not found in nature that adopt desired structures and perform novel functions. Although proteins could, in theory, be designed with ab initio methods, practical success has come from using large amounts of data that describe the sequences, structures, and functions of existing proteins and their variants. We present recent creative uses of multiple-sequence alignments, protein structures, and high-throughput functional assays in computational protein design. Approaches range from enhancing structure-based design with experimental data to building regression models to training deep neural nets that generate novel sequences. Looking ahead, deep learning will be increasingly important for maximizing the value of data for protein design.
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Affiliation(s)
- Vincent Frappier
- Generate Biomedicines, 26 Landsdowne Street, Cambridge, MA, 02139, USA
| | - Amy E Keating
- MIT Departments of Biology and Biological Engineering, 77 Massachusetts Ave., Cambridge, MA, 02139, USA.
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15
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Wang F, Gnewou O, Modlin C, Beltran LC, Xu C, Su Z, Juneja P, Grigoryan G, Egelman EH, Conticello VP. Structural analysis of cross α-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials. Nat Commun 2021; 12:407. [PMID: 33462223 PMCID: PMC7814010 DOI: 10.1038/s41467-020-20689-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Charles Modlin
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Leticia C Beltran
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Chunfu Xu
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Zhangli Su
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Puneet Juneja
- The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA, 30322, USA
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, NH, 03755, USA.,Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Vincent P Conticello
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA. .,The Robert P. Apkarian Integrated Electron Microscopy Core (IEMC), Emory University, Atlanta, GA, 30322, USA.
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16
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Miles JA, Hobor F, Trinh CH, Taylor J, Tiede C, Rowell PR, Jackson BR, Nadat FA, Ramsahye P, Kyle HF, Wicky BIM, Clarke J, Tomlinson DC, Wilson AJ, Edwards TA. Selective Affimers Recognise the BCL-2 Family Proteins BCL-x L and MCL-1 through Noncanonical Structural Motifs*. Chembiochem 2021; 22:232-240. [PMID: 32961017 PMCID: PMC7821230 DOI: 10.1002/cbic.202000585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/17/2020] [Indexed: 12/26/2022]
Abstract
The BCL-2 family is a challenging group of proteins to target selectively due to sequence and structural homologies across the family. Selective ligands for the BCL-2 family regulators of apoptosis are useful as probes to understand cell biology and apoptotic signalling pathways, and as starting points for inhibitor design. We have used phage display to isolate Affimer reagents (non-antibody-binding proteins based on a conserved scaffold) to identify ligands for MCL-1, BCL-xL , BCL-2, BAK and BAX, then used multiple biophysical characterisation methods to probe the interactions. We established that purified Affimers elicit selective recognition of their target BCL-2 protein. For anti-apoptotic targets BCL-xL and MCL-1, competitive inhibition of their canonical protein-protein interactions is demonstrated. Co-crystal structures reveal an unprecedented mode of molecular recognition; where a BH3 helix is normally bound, flexible loops from the Affimer dock into the BH3 binding cleft. Moreover, the Affimers induce a change in the target proteins towards a desirable drug-bound-like conformation. These proof-of-concept studies indicate that Affimers could be used as alternative templates to inspire the design of selective BCL-2 family modulators and more generally other protein-protein interaction inhibitors.
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Affiliation(s)
- Jennifer A. Miles
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Fruzsina Hobor
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Chi H. Trinh
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - James Taylor
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Christian Tiede
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Philip R. Rowell
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Brian R. Jackson
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Protein Production FacilityUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Fatima A. Nadat
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Protein Production FacilityUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Pallavi Ramsahye
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Hannah F. Kyle
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Basile I. M. Wicky
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Jane Clarke
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Darren C. Tomlinson
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Andrew J. Wilson
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Thomas A. Edwards
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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17
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Pan X, Kortemme T. Recent advances in de novo protein design: Principles, methods, and applications. J Biol Chem 2021; 296:100558. [PMID: 33744284 PMCID: PMC8065224 DOI: 10.1016/j.jbc.2021.100558] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
The computational de novo protein design is increasingly applied to address a number of key challenges in biomedicine and biological engineering. Successes in expanding applications are driven by advances in design principles and methods over several decades. Here, we review recent innovations in major aspects of the de novo protein design and include how these advances were informed by principles of protein architecture and interactions derived from the wealth of structures in the Protein Data Bank. We describe developments in de novo generation of designable backbone structures, optimization of sequences, design scoring functions, and the design of the function. The advances not only highlight design goals reachable now but also point to the challenges and opportunities for the future of the field.
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Affiliation(s)
- Xingjie Pan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA; UC Berkeley - UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, California, USA.
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA; UC Berkeley - UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, California, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California, USA.
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18
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Abstract
We describe the de novo design of an allosterically regulated protein, which comprises two tightly coupled domains. One domain is based on the DF (Due Ferri in Italian or two-iron in English) family of de novo proteins, which have a diiron cofactor that catalyzes a phenol oxidase reaction, while the second domain is based on PS1 (Porphyrin-binding Sequence), which binds a synthetic Zn-porphyrin (ZnP). The binding of ZnP to the original PS1 protein induces changes in structure and dynamics, which we expected to influence the catalytic rate of a fused DF domain when appropriately coupled. Both DF and PS1 are four-helix bundles, but they have distinct bundle architectures. To achieve tight coupling between the domains, they were connected by four helical linkers using a computational method to discover the most designable connections capable of spanning the two architectures. The resulting protein, DFP1 (Due Ferri Porphyrin), bound the two cofactors in the expected manner. The crystal structure of fully reconstituted DFP1 was also in excellent agreement with the design, and it showed the ZnP cofactor bound over 12 Å from the dimetal center. Next, a substrate-binding cleft leading to the diiron center was introduced into DFP1. The resulting protein acts as an allosterically modulated phenol oxidase. Its Michaelis-Menten parameters were strongly affected by the binding of ZnP, resulting in a fourfold tighter K m and a 7-fold decrease in k cat These studies establish the feasibility of designing allosterically regulated catalytic proteins, entirely from scratch.
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19
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Reddy CN, Manzar N, Ateeq B, Sankararamakrishnan R. Computational Design of BH3-Mimetic Peptide Inhibitors That Can Bind Specifically to Mcl-1 or Bcl-X L: Role of Non-Hot Spot Residues. Biochemistry 2020; 59:4379-4394. [PMID: 33146015 DOI: 10.1021/acs.biochem.0c00661] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Interactions between pro- and anti-apoptotic Bcl-2 proteins decide the fate of the cell. The BH3 domain of pro-apoptotic Bcl-2 proteins interacts with the exposed hydrophobic groove of their anti-apoptotic counterparts. Through their design and development, BH3 mimetics that target the hydrophobic groove of specific anti-apoptotic Bcl-2 proteins have the potential to become anticancer drugs. We have developed a novel computational method for designing sequences with BH3 domain features that can bind specifically to anti-apoptotic Mcl-1 or Bcl-XL. In this method, we retained the four highly conserved hydrophobic and aspartic residues of wild-type BH3 sequences and randomly substituted all other positions to generate a large number of BH3-like sequences. We modeled 20000 complex structures with Mcl-1 or Bcl-XL using the BH3-like sequences derived from five wild-type pro-apoptotic BH3 peptides. Peptide-protein interaction energies calculated from these models for each set of BH3-like sequences resulted in negatively skewed extreme value distributions. The selected BH3-like sequences from the extreme negative tail regions have highly favorable interaction energies with Mcl-1 or Bcl-XL. They are enriched in acidic and basic residues when they bind to Mcl-1 and Bcl-XL, respectively. With the charged residues often away from the binding interface, the overall electric field generated by the charged residues results in strong long-range electrostatic interaction energies between the peptide and the protein giving rise to high specificity. Cell viability studies of representative BH3-like peptides further validated the predicted specificity. This study has revealed the importance of non-hot spot residues in BH3-mimetic peptides in providing specificity to a particular anti-apoptotic protein.
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20
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Zhou J, Panaitiu AE, Grigoryan G. A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures. Proc Natl Acad Sci U S A 2020; 117:1059-1068. [PMID: 31892539 PMCID: PMC6969538 DOI: 10.1073/pnas.1908723117] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Current state-of-the-art approaches to computational protein design (CPD) aim to capture the determinants of structure from physical principles. While this has led to many successful designs, it does have strong limitations associated with inaccuracies in physical modeling, such that a reliable general solution to CPD has yet to be found. Here, we propose a design framework-one based on identifying and applying patterns of sequence-structure compatibility found in known proteins, rather than approximating them from models of interatomic interactions. We carry out extensive computational analyses and an experimental validation for our method. Our results strongly argue that the Protein Data Bank is now sufficiently large to enable proteins to be designed by using only examples of structural motifs from unrelated proteins. Because our method is likely to have orthogonal strengths relative to existing techniques, it could represent an important step toward removing remaining barriers to robust CPD.
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Affiliation(s)
- Jianfu Zhou
- Department of Computer Science, Dartmouth College, Hanover, NH 03755
| | | | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, NH 03755;
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
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21
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Kønig SM, Rissler V, Terkelsen T, Lambrughi M, Papaleo E. Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level. PLoS Comput Biol 2019; 15:e1007485. [PMID: 31825969 PMCID: PMC6927658 DOI: 10.1371/journal.pcbi.1007485] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/23/2019] [Accepted: 10/12/2019] [Indexed: 12/11/2022] Open
Abstract
Apoptosis is an essential defensive mechanism against tumorigenesis. Proteins of the B-cell lymphoma-2 (Bcl-2) family regulate programmed cell death by the mitochondrial apoptosis pathway. In response to intracellular stress, the apoptotic balance is governed by interactions of three distinct subgroups of proteins; the activator/sensitizer BH3 (Bcl-2 homology 3)-only proteins, the pro-survival, and the pro-apoptotic executioner proteins. Changes in expression levels, stability, and functional impairment of pro-survival proteins can lead to an imbalance in tissue homeostasis. Their overexpression or hyperactivation can result in oncogenic effects. Pro-survival Bcl-2 family members carry out their function by binding the BH3 short linear motif of pro-apoptotic proteins in a modular way, creating a complex network of protein-protein interactions. Their dysfunction enables cancer cells to evade cell death. The critical role of Bcl-2 proteins in homeostasis and tumorigenesis, coupled with mounting insight in their structural properties, make them therapeutic targets of interest. A better understanding of gene expression, mutational profile, and molecular mechanisms of pro-survival Bcl-2 proteins in different cancer types, could help to clarify their role in cancer development and may guide advancement in drug discovery. Here, we shed light on the pro-survival Bcl-2 proteins in breast cancer using different bioinformatic approaches, linking -omics with structural data. We analyzed the changes in the expression of the Bcl-2 proteins and their BH3-containing interactors in breast cancer samples. We then studied, at the structural level, a selection of interactions, accounting for effects induced by mutations found in the breast cancer samples. We find two complexes between the up-regulated Bcl2A1 and two down-regulated BH3-only candidates (i.e., Hrk and Nr4a1) as targets associated with reduced apoptosis in breast cancer samples for future experimental validation. Furthermore, we predict L99R, M75R as damaging mutations altering protein stability, and Y120C as a possible allosteric mutation from an exposed surface to the BH3-binding site.
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Affiliation(s)
- Simon Mathis Kønig
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Vendela Rissler
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Thilde Terkelsen
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
- Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
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22
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Kuhlman B, Bradley P. Advances in protein structure prediction and design. Nat Rev Mol Cell Biol 2019; 20:681-697. [PMID: 31417196 PMCID: PMC7032036 DOI: 10.1038/s41580-019-0163-x] [Citation(s) in RCA: 373] [Impact Index Per Article: 74.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2019] [Indexed: 12/18/2022]
Abstract
The prediction of protein three-dimensional structure from amino acid sequence has been a grand challenge problem in computational biophysics for decades, owing to its intrinsic scientific interest and also to the many potential applications for robust protein structure prediction algorithms, from genome interpretation to protein function prediction. More recently, the inverse problem - designing an amino acid sequence that will fold into a specified three-dimensional structure - has attracted growing attention as a potential route to the rational engineering of proteins with functions useful in biotechnology and medicine. Methods for the prediction and design of protein structures have advanced dramatically in the past decade. Increases in computing power and the rapid growth in protein sequence and structure databases have fuelled the development of new data-intensive and computationally demanding approaches for structure prediction. New algorithms for designing protein folds and protein-protein interfaces have been used to engineer novel high-order assemblies and to design from scratch fluorescent proteins with novel or enhanced properties, as well as signalling proteins with therapeutic potential. In this Review, we describe current approaches for protein structure prediction and design and highlight a selection of the successful applications they have enabled.
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Affiliation(s)
- Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
| | - Philip Bradley
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
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23
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Denis C, Sopková-de Oliveira Santos J, Bureau R, Voisin-Chiret AS. Hot-Spots of Mcl-1 Protein. J Med Chem 2019; 63:928-943. [DOI: 10.1021/acs.jmedchem.9b00983] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Camille Denis
- Normandie Univiversité, UNICAEN, CERMN, 14000 Caen, France
| | | | - Ronan Bureau
- Normandie Univiversité, UNICAEN, CERMN, 14000 Caen, France
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