1
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Martinsen E, Jinnurine T, Subramani S, Rogne M. Advances in RNA therapeutics for modulation of 'undruggable' targets. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 204:249-294. [PMID: 38458740 DOI: 10.1016/bs.pmbts.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
Over the past decades, drug discovery utilizing small pharmacological compounds, fragment-based therapeutics, and antibody therapy have significantly advanced treatment options for many human diseases. However, a major bottleneck has been that>70% of human proteins/genomic regions are 'undruggable' by the above-mentioned approaches. Many of these proteins constitute essential drug targets against complex multifactorial diseases like cancer, immunological disorders, and neurological diseases. Therefore, alternative approaches are required to target these proteins or genomic regions in human cells. RNA therapeutics is a promising approach for many of the traditionally 'undruggable' targets by utilizing methods such as antisense oligonucleotides, RNA interference, CRISPR/Cas-based genome editing, aptamers, and the development of mRNA therapeutics. In the following chapter, we will put emphasis on recent advancements utilizing these approaches against challenging drug targets, such as intranuclear proteins, intrinsically disordered proteins, untranslated genomic regions, and targets expressed in inaccessible tissues.
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Affiliation(s)
| | | | - Saranya Subramani
- Pioneer Research AS, Oslo Science Park, Oslo, Norway; Department of Pharmacy, Section for Pharmacology and Pharmaceutical Biosciences, University of Oslo, Oslo, Norway
| | - Marie Rogne
- Pioneer Research AS, Oslo Science Park, Oslo, Norway; Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
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2
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Chakraborty A, Hussain A, Sabnam N. Uncovering the structural stability of Magnaporthe oryzae effectors: a secretome-wide in silico analysis. J Biomol Struct Dyn 2023:1-22. [PMID: 38109060 DOI: 10.1080/07391102.2023.2292795] [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: 05/07/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023]
Abstract
Rice blast, caused by the ascomycete fungus Magnaporthe oryzae, is a deadly disease and a major threat to global food security. The pathogen secretes small proteinaceous effectors, virulence factors, inside the host to manipulate and perturb the host immune system, allowing the pathogen to colonize and establish a successful infection. While the molecular functions of several effectors are characterized, very little is known about the structural stability of these effectors. We analyzed a total of 554 small secretory proteins (SSPs) from the M. oryzae secretome to decipher key features of intrinsic disorder (ID) and the structural dynamics of the selected putative effectors through thorough and systematic in silico studies. Our results suggest that out of the total SSPs, 66% were predicted as effector proteins, released either into the apoplast or cytoplasm of the host cell. Of these, 68% were found to be intrinsically disordered effector proteins (IDEPs). Among the six distinct classes of disordered effectors, we observed peculiar relationships between the localization of several effectors in the apoplast or cytoplasm and the degree of disorder. We determined the degree of structural disorder and its impact on protein foldability across all the putative small secretory effector proteins from the blast pathogen, further validated by molecular dynamics simulation studies. This study provides definite clues toward unraveling the mystery behind the importance of structural distortions in effectors and their impact on plant-pathogen interactions. The study of these dynamical segments may help identify new effectors as well.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Afzal Hussain
- Department of Bioinformatics, Maulana Azad National Institute of Technology, Bhopal, India
| | - Nazmiara Sabnam
- Department of Life Sciences, Presidency University, Kolkata, India
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3
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Patalano SD, Fuxman Bass P, Fuxman Bass JI. Transcription factors in the development and treatment of immune disorders. Transcription 2023:1-23. [PMID: 38100543 DOI: 10.1080/21541264.2023.2294623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023] Open
Abstract
Immune function is highly controlled at the transcriptional level by the binding of transcription factors (TFs) to promoter and enhancer elements. Several TF families play major roles in immune gene expression, including NF-κB, STAT, IRF, AP-1, NRs, and NFAT, which trigger anti-pathogen responses, promote cell differentiation, and maintain immune system homeostasis. Aberrant expression, activation, or sequence of isoforms and variants of these TFs can result in autoimmune and inflammatory diseases as well as hematological and solid tumor cancers. For this reason, TFs have become attractive drug targets, even though most were previously deemed "undruggable" due to their lack of small molecule binding pockets and the presence of intrinsically disordered regions. However, several aspects of TF structure and function can be targeted for therapeutic intervention, such as ligand-binding domains, protein-protein interactions between TFs and with cofactors, TF-DNA binding, TF stability, upstream signaling pathways, and TF expression. In this review, we provide an overview of each of the important TF families, how they function in immunity, and some related diseases they are involved in. Additionally, we discuss the ways of targeting TFs with drugs along with recent research developments in these areas and their clinical applications, followed by the advantages and disadvantages of targeting TFs for the treatment of immune disorders.
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Affiliation(s)
- Samantha D Patalano
- Biology Department, Boston University, Boston, MA, USA
- Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Paula Fuxman Bass
- Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Juan I Fuxman Bass
- Biology Department, Boston University, Boston, MA, USA
- Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
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4
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Staerz S, Lisabeth EM, Njomen E, Dexheimer TS, Neubig RR, Tepe JJ. Development of a Cell-Based AlphaLISA Assay for High-Throughput Screening for Small Molecule Proteasome Modulators. ACS OMEGA 2023; 8:15650-15659. [PMID: 37151549 PMCID: PMC10157846 DOI: 10.1021/acsomega.3c01158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/12/2023] [Indexed: 05/09/2023]
Abstract
The balance between protein degradation and protein synthesis is a highly choreographed process generally called proteostasis. Most intracellular protein degradation occurs through the ubiquitin-proteasome system (UPS). This degradation takes place through either a ubiquitin-dependent or a ubiquitin-independent proteasomal pathway. The ubiquitin-independent pathway selectively targets unfolded proteins, including intrinsically disordered proteins (IDPs). Dysregulation of proteolysis can lead to the accumulation of IDPs, seen in the pathogenesis of various diseases, including cancer and neurodegeneration. Therefore, the enhancement of the proteolytic activity of the 20S proteasome using small molecules has been identified as a promising pathway to combat IDP accumulation. Currently, there are a limited number of known small molecules that enhance the activity of the 20S proteasome, and few are observed to exhibit enhanced proteasome activity in cell culture. Herein, we describe the development of a high-throughput screening assay to identify cell-permeable proteasome enhancers by utilizing an AlphaLISA platform that measures the degradation of a GFP conjugated intrinsically disordered protein, ornithine decarboxylase (ODC). Through the screening of the Prestwick and NIH Clinical Libraries, a kinase inhibitor, erlotinib, was identified as a new 20S proteasome enhancer, which enhances the degradation of ODC in cells and α-synuclein in vitro.
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Affiliation(s)
- Sophia
D. Staerz
- Department
of Chemistry, Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Erika M. Lisabeth
- Department
of Chemistry, Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Evert Njomen
- Department
of Chemistry, Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas S. Dexheimer
- Department
of Chemistry, Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Richard R. Neubig
- Department
of Chemistry, Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jetze J. Tepe
- Department
of Chemistry, Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan 48824, United States
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5
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Kovács D, Bodor A. The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs. RSC Adv 2023; 13:10182-10203. [PMID: 37006359 PMCID: PMC10065145 DOI: 10.1039/d3ra00977g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
In studying secondary structural propensities of proteins by nuclear magnetic resonance (NMR) spectroscopy, secondary chemical shifts (SCSs) serve as the primary atomic scale observables. For SCS calculation, the selection of an appropriate random coil chemical shift (RCCS) dataset is a crucial step, especially when investigating intrinsically disordered proteins (IDPs). The scientific literature is abundant in such datasets, however, the effect of choosing one over all the others in a concrete application has not yet been studied thoroughly and systematically. Hereby, we review the available RCCS prediction methods and to compare them, we conduct statistical inference by means of the nonparametric sum of ranking differences and comparison of ranks to random numbers (SRD-CRRN) method. We try to find the RCCS predictors best representing the general consensus regarding secondary structural propensities. The existence and the magnitude of resulting differences on secondary structure determination under varying sample conditions (temperature, pH) are demonstrated and discussed for globular proteins and especially IDPs.
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Affiliation(s)
- Dániel Kovács
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
- Eötvös Loránd University, Hevesy György PhD School of Chemistry Pázmány Péter sétány 1/A Budapest 1117 Hungary
| | - Andrea Bodor
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
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6
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Lee KY, Lee BJ. Dynamics-Based Regulatory Switches of Type II Antitoxins: Insights into New Antimicrobial Discovery. Antibiotics (Basel) 2023; 12:antibiotics12040637. [PMID: 37106997 PMCID: PMC10135005 DOI: 10.3390/antibiotics12040637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Type II toxin-antitoxin (TA) modules are prevalent in prokaryotes and are involved in cell maintenance and survival under harsh environmental conditions, including nutrient deficiency, antibiotic treatment, and human immune responses. Typically, the type II TA system consists of two protein components: a toxin that inhibits an essential cellular process and an antitoxin that neutralizes its toxicity. Antitoxins of type II TA modules typically contain the structured DNA-binding domain responsible for TA transcription repression and an intrinsically disordered region (IDR) at the C-terminus that directly binds to and neutralizes the toxin. Recently accumulated data have suggested that the antitoxin's IDRs exhibit variable degrees of preexisting helical conformations that stabilize upon binding to the corresponding toxin or operator DNA and function as a central hub in regulatory protein interaction networks of the type II TA system. However, the biological and pathogenic functions of the antitoxin's IDRs have not been well discussed compared with those of IDRs from the eukaryotic proteome. Here, we focus on the current state of knowledge about the versatile roles of IDRs of type II antitoxins in TA regulation and provide insights into the discovery of new antibiotic candidates that induce toxin activation/reactivation and cell death by modulating the regulatory dynamics or allostery of the antitoxin.
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Affiliation(s)
- Ki-Young Lee
- College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Pocheon-si 11160, Republic of Korea
| | - Bong-Jin Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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7
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Kabra A, Bushweller J. The Intrinsically Disordered Proteins MLLT3 (AF9) and MLLT1 (ENL) - Multimodal Transcriptional Switches With Roles in Normal Hematopoiesis, MLL Fusion Leukemia, and Kidney Cancer. J Mol Biol 2022; 434:167117. [PMID: 34174329 PMCID: PMC8695629 DOI: 10.1016/j.jmb.2021.167117] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/17/2021] [Accepted: 06/17/2021] [Indexed: 01/17/2023]
Abstract
AF9 (MLLT3) and ENL (MLLT1) are members of the YEATS family (named after the five proteins first shown to contain this domain: Yaf9, ENL, AF9, Taf14, Sas5) defined by the presence of a YEATS domain. The YEATS domain is an epigenetic reader that binds to acetylated and crotonylated lysines, unlike the bromodomain which can only bind to acetylated lysines. All members of this family have been shown to be components of various complexes with roles in chromatin remodeling, histone modification, histone variant deposition, and transcriptional regulation. MLLT3 is a critical regulator of hematopoiesis with a role in maintaining the hematopoietic stem or progenitor cell (HSPC) population. Approximately 10% of acute myeloid leukemia (AML) and acute lymphocytic leukemia (ALL) patients harbor a translocation involving MLL (mixed lineage leukemia). In the context of MLL fusion patients with AML and ALL, MLL-AF9 and MLL-ENL fusions are observed in 34 and 31% of the patients, respectively. The intrinsically disordered C-terminal domain of MLLT3 (AHD, ANC1 homology domain) undergoes coupled binding and folding upon interaction with partner proteins AF4, DOT1L, BCOR, and CBX8. Backbone dynamics studies of the complexes suggest a role for dynamics in function. Inhibitors of the interaction of the intrinsically disordered AHD with partner proteins have been described, highlighting the feasibility of targeting intrinsically disordered regions. MLLT1 undergoes phase separation to enhance recruitment of the super elongation complex (SEC) and drive transcription. Mutations in MLLT1 observed in Wilms tumor patients enhance phase separation and transcription to drive an aberrant gene expression program.
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Affiliation(s)
- Ashish Kabra
- Dept. of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, United States
| | - John Bushweller
- Dept. of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, United States; Dept. of Chemistry, University of Virginia, Charlottesville, VA 22904, United States.
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8
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Su BG, Henley MJ. Drugging Fuzzy Complexes in Transcription. Front Mol Biosci 2022; 8:795743. [PMID: 34993233 PMCID: PMC8724552 DOI: 10.3389/fmolb.2021.795743] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription factors (TFs) are one of the most promising but underutilized classes of drug targets. The high degree of intrinsic disorder in both the structure and the interactions (i.e., “fuzziness”) of TFs is one of the most important challenges to be addressed in this context. Here, we discuss the impacts of fuzziness on transcription factor drug discovery, describing how disorder poses fundamental problems to the typical drug design, and screening approaches used for other classes of proteins such as receptors or enzymes. We then speculate on ways modern biophysical and chemical biology approaches could synergize to overcome many of these challenges by directly addressing the challenges imposed by TF disorder and fuzziness.
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Affiliation(s)
- Bonnie G Su
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States.,The Broad Institute of MIT and Harvard, Cambridge, MA, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Matthew J Henley
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States.,The Broad Institute of MIT and Harvard, Cambridge, MA, United States
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9
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Therapeutics-how to treat phase separation-associated diseases. Emerg Top Life Sci 2021; 4:307-318. [PMID: 32364240 PMCID: PMC7733670 DOI: 10.1042/etls20190176] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 12/16/2022]
Abstract
Liquid-liquid phase separation has drawn attention as many neurodegeneration or cancer-associated proteins are able to form liquid membraneless compartments (condensates) by liquid-liquid phase separation. Furthermore, there is rapidly growing evidence that disease-associated mutation or post-translational modification of these proteins causes aberrant location, composition or physical properties of the condensates. It is ambiguous whether aberrant condensates are always causative in disease mechanisms, however they are likely promising potential targets for therapeutics. The conceptual framework of liquid-liquid phase separation provides opportunities for novel therapeutic approaches. This review summarises how the extensive recent advances in understanding control of nucleation, growth and composition of condensates by protein post-translational modification has revealed many possibilities for intervention by conventional small molecule enzyme inhibitors. This includes the first proof-of-concept examples. However, understanding membraneless organelle formation as a physical chemistry process also highlights possible physicochemical mechanisms of intervention. There is huge demand for innovation in drug development, especially for challenging diseases of old age including neurodegeneration and cancer. The conceptual framework of liquid-liquid phase separation provides a new paradigm for thinking about modulating protein function and is very different from enzyme lock-and-key or structured binding site concepts and presents new opportunities for innovation.
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10
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Radaeva M, Ton AT, Hsing M, Ban F, Cherkasov A. Drugging the 'undruggable'. Therapeutic targeting of protein-DNA interactions with the use of computer-aided drug discovery methods. Drug Discov Today 2021; 26:2660-2679. [PMID: 34332092 DOI: 10.1016/j.drudis.2021.07.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/22/2021] [Accepted: 07/17/2021] [Indexed: 02/09/2023]
Abstract
Transcription factors (TFs) act as major oncodrivers in many cancers and are frequently regarded as high-value therapeutic targets. The functionality of TFs relies on direct protein-DNA interactions, which are notoriously difficult to target with small molecules. However, this prior view of the 'undruggability' of protein-DNA interfaces has shifted substantially in recent years, in part because of significant advances in computer-aided drug discovery (CADD). In this review, we highlight recent examples of successful CADD campaigns resulting in drug candidates that directly interfere with protein-DNA interactions of several key cancer TFs, including androgen receptor (AR), ETS-related gene (ERG), MYC, thymocyte selection-associated high mobility group box protein (TOX), topoisomerase II (TOP2), and signal transducer and activator of transcription 3 (STAT3). Importantly, these findings open novel and compelling avenues for therapeutic targeting of over 1600 human TFs implicated in many conditions including and beyond cancer.
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Affiliation(s)
- Mariia Radaeva
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Anh-Tien Ton
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Michael Hsing
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada.
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11
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Oh S, Lee MK, Chi SW. Single-molecule analysis of interaction between p53TAD and MDM2 using aerolysin nanopores. Chem Sci 2021; 12:5883-5891. [PMID: 34168813 PMCID: PMC8179679 DOI: 10.1039/d1sc00386k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Protein-protein interactions (PPIs) are regarded as important, but undruggable targets. Intrinsically disordered p53 transactivation domain (p53TAD) mediates PPI with mouse double minute 2 (MDM2), which is an attractive anticancer target for therapeutic intervention. Here, using aerolysin nanopores, we probed the p53TAD peptide/MDM2 interaction and its modulation by small-molecule PPI inhibitors or p53TAD phosphorylation. Although the p53TAD peptide showed short-lived (<100 ms) translocation, the protein complex induced the characteristic extraordinarily long-lived (0.1 s ∼ tens of min) current blockage, indicating that the MDM2 recruitment by p53TAD peptide almost fully occludes the pore. Simultaneously, the protein complex formation substantially reduced the event frequency of short-lived peptide translocation. Notably, the addition of small-molecule PPI inhibitors, Nutlin-3 and AMG232, or Thr18 phosphorylation of p53TAD peptide, were able to diminish the extraordinarily long-lived events and restore the short-lived translocation of the peptide rescued from the complex. Taken together, our results elucidate a novel mechanism of single-molecule sensing for analyzing PPIs and their inhibitors using aerolysin nanopores. This novel methodology may contribute to remarkable improvements in drug discovery targeted against undruggable PPIs.
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Affiliation(s)
- Sohee Oh
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology Daejeon 34113 Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology Daejeon 34113 Republic of Korea
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology Daejeon 34141 Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology Daejeon 34113 Republic of Korea
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12
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Li J, Zhang Y, Chen X, Ma L, Li P, Yu H. Protein phase separation and its role in chromatin organization and diseases. Biomed Pharmacother 2021; 138:111520. [PMID: 33765580 DOI: 10.1016/j.biopha.2021.111520] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/04/2021] [Accepted: 03/14/2021] [Indexed: 12/25/2022] Open
Abstract
In the physical sciences, solid, liquid, and gas are the most familiar phase states, whose essence is their existence reflecting the different spatial distribution of molecular components. The biological molecules in the living cell also have differences in spatial distribution. The molecules organized in the form of membrane-bound organelles are well recognized. However, the biomolecules organized in membraneless compartments called biomolecular condensates remain elusive. The liquid-liquid phase separation (LLPS), as a new emerging scientific breakthrough, describes the biomolecules assembled in special distribution and appeared as membraneless condensates in the form of a new "phase" compared with the surrounding liquid milieu. LLPS provides an important theoretical basis for explaining the composition of biological molecules and related biological reactions. Mounting evidence has emerged recently that phase-separated condensates participate in various biological activities. This article reviews the occurrence of LLPS and underlying regulatory mechanisms for understanding how multivalent molecules drive phase transitions to form the biomolecular condensates. And, it also summarizes recent major progress in elucidating the roles of LLPS in chromatin organization and provides clues for the development of new innovative therapeutic strategies for related diseases.
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Affiliation(s)
- Jiaqi Li
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Yao Zhang
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Xi Chen
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Lijuan Ma
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Haijie Yu
- Dr. Neher's Laboratory for innovative Drug Discovery, Macau University of Science and Technology, Macao, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, China.
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13
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Chong B, Yang Y, Wang ZL, Xing H, Liu Z. Reinforcement learning to boost molecular docking upon protein conformational ensemble. Phys Chem Chem Phys 2021; 23:6800-6806. [PMID: 33724276 DOI: 10.1039/d0cp06378a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) are widely involved in human diseases and thus are attractive therapeutic targets. In practice, however, it is computationally prohibitive to dock large ligand libraries to thousands and tens of thousands of conformations. Here, we propose a reversible upper confidence bound (UCB) algorithm for the virtual screening of IDPs to address the influence of the conformation ensemble. The docking process is dynamically arranged so that attempts are focused near the boundary to separate top ligands from the bulk accurately. It is demonstrated in the example of transcription factor c-Myc that the average docking number per ligand can be greatly reduced while the performance is merely slightly affected. This study suggests that reinforcement learning is highly efficient in solving the bottleneck of virtual screening due to the conformation ensemble in the rational drug design of IDPs.
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Affiliation(s)
- Bin Chong
- College of Chemistry and Molecular Engineering, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China.
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14
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Chong B, Yang Y, Zhou C, Huang Q, Liu Z. Ensemble-Based Thermodynamics of the Fuzzy Binding between Intrinsically Disordered Proteins and Small-Molecule Ligands. J Chem Inf Model 2020; 60:4967-4974. [PMID: 33054197 DOI: 10.1021/acs.jcim.0c00963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In contrast to the "lock-and-key" model underlying the long-term success of structural biology and rational drug design, intrinsically disordered proteins (IDPs) exist in an ensemble of highly heterogeneous conformations even after binding with small-molecule ligands. It remains controversial how to characterize the thermodynamics of such fuzzy interactions. Here, we derive an ensemble-based thermodynamic framework to analyze the apparent affinity between IDPs and ligands. It is shown that the apparent affinity is related to the interaction free energy between the individual conformation and ligand in a way similar to Jarzynski's equality in nonequilibrium statistics. The oncoprotein c-Myc is adopted as an example to demonstrate the related properties, for example, the distribution of conformation-ligand interaction free energy, the entropic contribution from the ensemble, the conformation shift under ligand binding, and how to control the error under a limited number of sampled conformations.
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Affiliation(s)
- Bin Chong
- College of Chemistry and Molecular Engineering, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China
| | - Yingguang Yang
- School of Cyberscience, University of Science and Technology of China, Hefei 230026, China
| | - Chenguang Zhou
- College of Chemistry and Molecular Engineering, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China
| | - Qiaojing Huang
- College of Chemistry and Molecular Engineering, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China
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15
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Chen J, Liu X, Chen J. Targeting Intrinsically Disordered Proteins through Dynamic Interactions. Biomolecules 2020; 10:E743. [PMID: 32403216 PMCID: PMC7277182 DOI: 10.3390/biom10050743] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/04/2020] [Accepted: 05/09/2020] [Indexed: 12/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are over-represented in major disease pathways and have attracted significant interest in understanding if and how they may be targeted using small molecules for therapeutic purposes. While most existing studies have focused on extending the traditional structure-centric drug design strategies and emphasized exploring pre-existing structure features of IDPs for specific binding, several examples have also emerged to suggest that small molecules could achieve specificity in binding IDPs and affect their function through dynamic and transient interactions. These dynamic interactions can modulate the disordered conformational ensemble and often lead to modest compaction to shield functionally important interaction sites. Much work remains to be done on further elucidation of the molecular basis of the dynamic small molecule-IDP interaction and determining how it can be exploited for targeting IDPs in practice. These efforts will rely critically on an integrated experimental and computational framework for disordered protein ensemble characterization. In particular, exciting advances have been made in recent years in enhanced sampling techniques, Graphic Processing Unit (GPU)-computing, and protein force field optimization, which have now allowed rigorous physics-based atomistic simulations to generate reliable structure ensembles for nontrivial IDPs of modest sizes. Such de novo atomistic simulations will play crucial roles in exploring the exciting opportunity of targeting IDPs through dynamic interactions.
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Affiliation(s)
- Jianlin Chen
- Department of Hematology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou 318000, Zhejiang, China;
| | - Xiaorong Liu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA;
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA;
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
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16
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Sadar MD. Discovery of drugs that directly target the intrinsically disordered region of the androgen receptor. Expert Opin Drug Discov 2020; 15:551-560. [PMID: 32100577 DOI: 10.1080/17460441.2020.1732920] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Intrinsically disordered proteins (IDPs) and regions (IDRs) lack stable three-dimensional structure making drug discovery challenging. A validated therapeutic target for diseases such as prostate cancer is the androgen receptor (AR) which has a disordered amino-terminal domain (NTD) that contains all of its transcriptional activity. Drug discovery against the AR-NTD is of intense interest as a potential treatment for disease such as advanced prostate cancer that is driven by truncated constitutively active splice variants of AR that lack the C-terminal ligand-binding domain (LBD).Areas covered: This article presents an overview of the relevance of AR and its intrinsically disordered NTD as a drug target. AR structure and approaches to blocking AR transcriptional activity are discussed. The discovery of small molecules, including the libraries used, proven binders to the AR-NTD, and site of interaction of these small molecules in the AR-NTD are presented along with discussion of the Phase I clinical trial.Expert opinion: The lack of drugs in the clinic that directly bind IDPs/IDRs reflects the difficulty of targeting these proteins and obtaining specificity. However, it may also point to an inappropriateness of too closely borrowing concepts and resources from drug discovery to folded proteins.
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Affiliation(s)
- Marianne D Sadar
- Genome Sciences, BC Cancer and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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17
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Dynamic conformational flexibility and molecular interactions of intrinsically disordered proteins. J Biosci 2020. [DOI: 10.1007/s12038-020-0010-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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18
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Bhattarai A, Emerson IA. Dynamic conformational flexibility and molecular interactions of intrinsically disordered proteins. J Biosci 2020; 45:29. [PMID: 32020911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Intrinsically disordered proteins (IDPs) are highly flexible and undergo disorder to order transition upon binding. They are highly abundant in human proteomes and play critical roles in cell signaling and regulatory processes. This review mainly focuses on the dynamics of disordered proteins including their conformational heterogeneity, protein-protein interactions, and the phase transition of biomolecular condensates that are central to various biological functions. Besides, the role of RNA-mediated chaperones in protein folding and stability of IDPs were also discussed. Finally, we explored the dynamic binding interface of IDPs as novel therapeutic targets and the effect of small molecules on their interactions.
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Affiliation(s)
- Anil Bhattarai
- Bioinformatics Programming Laboratory, Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore 632 014, India
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19
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Abstract
Mutated or dysregulated transcription factors represent a unique class of drug targets that mediate aberrant gene expression, including blockade of differentiation and cell death gene expression programmes, hallmark properties of cancers. Transcription factor activity is altered in numerous cancer types via various direct mechanisms including chromosomal translocations, gene amplification or deletion, point mutations and alteration of expression, as well as indirectly through non-coding DNA mutations that affect transcription factor binding. Multiple approaches to target transcription factor activity have been demonstrated, preclinically and, in some cases, clinically, including inhibition of transcription factor-cofactor protein-protein interactions, inhibition of transcription factor-DNA binding and modulation of levels of transcription factor activity by altering levels of ubiquitylation and subsequent proteasome degradation or by inhibition of regulators of transcription factor expression. In addition, several new approaches to targeting transcription factors have recently emerged including modulation of auto-inhibition, proteolysis targeting chimaeras (PROTACs), use of cysteine reactive inhibitors, targeting intrinsically disordered regions of transcription factors and combinations of transcription factor inhibitors with kinase inhibitors to block the development of resistance. These innovations in drug development hold great promise to yield agents with unique properties that are likely to impact future cancer treatment.
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Affiliation(s)
- John H Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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20
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Oláh J, Ovádi J. Pharmacological targeting of α-synuclein and TPPP/p25 in Parkinson's disease: challenges and opportunities in a Nutshell. FEBS Lett 2019; 593:1641-1653. [PMID: 31148150 DOI: 10.1002/1873-3468.13464] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 01/10/2023]
Abstract
With the aging of population, neurological disorders, and especially disorders involving defects in protein conformation (also known as proteopathies) pose a serious socio-economic problem. So far there is no effective treatment for most proteopathies, including Parkinson's disease (PD). The mechanism underlying PD pathogenesis is largely unknown, and the hallmark proteins, α-synuclein (SYN) and tubulin polymerization promoting protein (TPPP/p25) are challenging drug targets. These proteins are intrinsically disordered with high conformational plasticity, and have diverse physiological and pathological functions. In the healthy brain, SYN and TPPP/p25 occur in neurons and oligodendrocytes, respectively; however, in PD and multiple system atrophy, they are co-enriched and co-localized in both cell types, thereby marking pathogenesis. Although large inclusions appear at a late disease stage, small, soluble assemblies of SYN promoted by TPPP/p25 are pathogenic. In the light of these issues, we established a new innovative strategy for the validation of a specific drug target based upon the identification of contact surfaces of the pathological SYN-TPPP/p25 complex that may lead to the development of peptidomimetic foldamers suitable for pharmaceutical intervention.
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Affiliation(s)
- Judit Oláh
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Judit Ovádi
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
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21
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Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins. Biomolecules 2019; 9:biom9040146. [PMID: 30979035 PMCID: PMC6523529 DOI: 10.3390/biom9040146] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 01/09/2023] Open
Abstract
Intrinsically disordered proteins (IDP) are abundant in the human genome and have recently emerged as major therapeutic targets for various diseases. Unlike traditional proteins that adopt a definitive structure, IDPs in free solution are disordered and exist as an ensemble of conformations. This enables the IDPs to signal through multiple signaling pathways and serve as scaffolds for multi-protein complexes. The challenge in studying IDPs experimentally stems from their disordered nature. Nuclear magnetic resonance (NMR), circular dichroism, small angle X-ray scattering, and single molecule Förster resonance energy transfer (FRET) can give the local structural information and overall dimension of IDPs, but seldom provide a unified picture of the whole protein. To understand the conformational dynamics of IDPs and how their structural ensembles recognize multiple binding partners and small molecule inhibitors, knowledge-based and physics-based sampling techniques are utilized in-silico, guided by experimental structural data. However, efficient sampling of the IDP conformational ensemble requires traversing the numerous degrees of freedom in the IDP energy landscape, as well as force-fields that accurately model the protein and solvent interactions. In this review, we have provided an overview of the current state of computational methods for studying IDP structure and dynamics and discussed the major challenges faced in this field.
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22
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Veras Ribeiro Filho H, Tambones IL, Mariano Gonçalves Dias M, Bernardi Videira N, Bruder M, Amorim Amato A, Migliorini Figueira AC. Modulation of nuclear receptor function: Targeting the protein-DNA interface. Mol Cell Endocrinol 2019; 484:1-14. [PMID: 30703486 DOI: 10.1016/j.mce.2019.01.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 02/02/2023]
Abstract
Nuclear receptors (NRs) are a superfamily of ligand-dependent transcription factors that modulate several biological processes. Traditionally, modulation of NRs has been focused on the development of ligands that recognize and bind to the ligand binding domain (LBD), resulting in activation or repression of transcription through the recruitment of coregulators. However, for more severe diseases, such as breast and prostate cancer, the conventional treatment addressing LBD modulation is not always successful, due to tumor resistance. To overcome these challenges and aiming to modulate NR activity by inhibiting the NR-DNA interaction, new studies focus on the development of molecules targeting alternative sites and domains on NRs. Here, we discuss two different approaches for this alternative NR modulation: one targeting the NR DNA binding domain (DBD); and the other targeting the DNA sites recognized by NRs. Our aim is to present the challenges and perspectives for developing specific inhibitors for each purpose, alongside with already reported examples.
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Affiliation(s)
- Helder Veras Ribeiro Filho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil; Graduate Program in Biosciences and Technology of Bioactive Products, Institute of Biology, State University of Campinas (Unicamp), Campinas, 13083-970, Brazil
| | - Izabella Luisa Tambones
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil; Graduate Program in Biosciences and Technology of Bioactive Products, Institute of Biology, State University of Campinas (Unicamp), Campinas, 13083-970, Brazil
| | - Marieli Mariano Gonçalves Dias
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil; Graduate Program in Molecular and Functional Biology, Institute of Biology, State University of Campinas (Unicamp), Campinas, SP, 13083-970, Brazil
| | - Natalia Bernardi Videira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil
| | - Marjorie Bruder
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil
| | - Angélica Amorim Amato
- Laboratory of Molecular Pharmacology, Department of Pharmaceutical Science, University of Brasilia (UnB), Brasília, DF, 70910-900, Brazil
| | - Ana Carolina Migliorini Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil.
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23
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Martinelli AHS, Lopes FC, John EBO, Carlini CR, Ligabue-Braun R. Modulation of Disordered Proteins with a Focus on Neurodegenerative Diseases and Other Pathologies. Int J Mol Sci 2019; 20:ijms20061322. [PMID: 30875980 PMCID: PMC6471803 DOI: 10.3390/ijms20061322] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/03/2019] [Accepted: 02/12/2019] [Indexed: 12/15/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) do not have rigid 3D structures, showing changes in their folding depending on the environment or ligands. Intrinsically disordered proteins are widely spread in eukaryotic genomes, and these proteins participate in many cell regulatory metabolism processes. Some IDPs, when aberrantly folded, can be the cause of some diseases such as Alzheimer′s, Parkinson′s, and prionic, among others. In these diseases, there are modifications in parts of the protein or in its entirety. A common conformational variation of these IDPs is misfolding and aggregation, forming, for instance, neurotoxic amyloid plaques. In this review, we discuss some IDPs that are involved in neurodegenerative diseases (such as beta amyloid, alpha synuclein, tau, and the “IDP-like” PrP), cancer (p53, c-Myc), and diabetes (amylin), focusing on the structural changes of these IDPs that are linked to such pathologies. We also present the IDP modulation mechanisms that can be explored in new strategies for drug design. Lastly, we show some candidate drugs that can be used in the future for the treatment of diseases caused by misfolded IDPs, considering that cancer therapy has more advanced research in comparison to other diseases, while also discussing recent and future developments in this area of research. Therefore, we aim to provide support to the study of IDPs and their modulation mechanisms as promising approaches to combat such severe diseases.
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Affiliation(s)
- Anne H S Martinelli
- Department of Molecular Biology and Biotechnology & Department of Biophysics, Biosciences Institute-IB, (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Fernanda C Lopes
- Center for Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Elisa B O John
- Center for Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Célia R Carlini
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Medicine and Health Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 91410-000, RS, Brazil.
- Brain Institute-InsCer, Laboratory of Neurotoxins, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil.
| | - Rodrigo Ligabue-Braun
- Department of Pharmaceutical Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre CEP 90050-170, RS, Brazil.
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24
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25
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Kiss R, Csizmadia G, Solti K, Keresztes A, Zhu M, Pickhardt M, Mandelkow E, Tóth G. Structural Basis of Small Molecule Targetability of Monomeric Tau Protein. ACS Chem Neurosci 2018; 9:2997-3006. [PMID: 29944336 DOI: 10.1021/acschemneuro.8b00182] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The therapeutic targeting of intrinsically disordered proteins (IDPs) by small molecules has been a challenge due to their heterogeneous conformational ensembles. A potential therapeutic strategy to alleviate the aggregation of IDPs is to maintain them in their native monomeric state by small molecule binding. This study investigates the structural basis of small molecule druggability of native monomeric Tau whose aggregation is linked to the onset of Tauopathies such as Alzheimer's disease. Initially, two available monomeric conformational ensembles of a shorter Tau construct K18 (also termed Tau4RD) were analyzed which revealed striking structural differences between the two ensembles, while similar number of hot spots and small molecule binding sites were identified on monomeric Tau ensembles as on tertiary folded proteins of similar size. Remarkably, some critical fibril forming sequence regions of Tau (V306-K311, V275-K280) participated in hot spot formation with higher frequency compared to other regions. As an example of small molecule binding to monomeric Tau, it was shown that methylene blue (MB) bound to monomeric K18 and full-length Tau selectively with high affinity (Kd = 125.8 nM and 86.6 nM, respectively) with binding modes involving Cys291 and Cys322, previously reported to be oxidized in the presence of MB. Overall, our results provide structure-based evidence that Tau can be a viable drug target for small molecules and indicate that specific small molecules may be able to bind to monomeric Tau and influence the way in which the protein interacts among itself and with other proteins.
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Affiliation(s)
- Róbert Kiss
- MTA-TTK-NAP B - Drug Discovery Research Group − Neurodegenerative Diseases, Institute of Organic Chemistry, Research Center for Natural Sciences, Hungarian Academy of Sciences, 1245 Budapest, Hungary
| | - Georgina Csizmadia
- MTA-TTK-NAP B - Drug Discovery Research Group − Neurodegenerative Diseases, Institute of Organic Chemistry, Research Center for Natural Sciences, Hungarian Academy of Sciences, 1245 Budapest, Hungary
| | - Katalin Solti
- MTA-TTK-NAP B - Drug Discovery Research Group − Neurodegenerative Diseases, Institute of Organic Chemistry, Research Center for Natural Sciences, Hungarian Academy of Sciences, 1245 Budapest, Hungary
| | - Attila Keresztes
- MTA-TTK-NAP B - Drug Discovery Research Group − Neurodegenerative Diseases, Institute of Organic Chemistry, Research Center for Natural Sciences, Hungarian Academy of Sciences, 1245 Budapest, Hungary
| | - Max Zhu
- Cantabio Pharmaceuticals, Sunnyvale, California 94085, United States
| | - Marcus Pickhardt
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Sigmund-Freud-Str. 27, 53127 Bonn, Germany
- CAESAR Research Center/Max-Planck-Institute, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Eckhard Mandelkow
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Sigmund-Freud-Str. 27, 53127 Bonn, Germany
- CAESAR Research Center/Max-Planck-Institute, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Gergely Tóth
- MTA-TTK-NAP B - Drug Discovery Research Group − Neurodegenerative Diseases, Institute of Organic Chemistry, Research Center for Natural Sciences, Hungarian Academy of Sciences, 1245 Budapest, Hungary
- Cantabio Pharmaceuticals, Sunnyvale, California 94085, United States
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26
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Chong B, Li M, Li T, Yu M, Zhang Y, Liu Z. Conservation of Potentially Druggable Cavities in Intrinsically Disordered Proteins. ACS OMEGA 2018; 3:15643-15652. [PMID: 31458221 PMCID: PMC6643371 DOI: 10.1021/acsomega.8b02092] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/05/2018] [Indexed: 05/08/2023]
Abstract
Intrinsically disordered proteins (IDPs) exist in highly dynamic conformational ensembles, which pose a major obstacle for drug development targeting IDPs because traditional rational drug design relies on unique three-dimensional structures. Here, we analyzed the conservation (especially structural conservation) of potentially druggable cavities in 22 ensembles of IDPs. It was found that there is considerable conservation for potentially druggable cavities within each ensemble. The average common atom percentage of potentially druggable cavities is as high as 54%. The average root-mean-squared deviation of common atoms ranges between 1 and 8 Å for multichain IDPs, and a common pocket is kept after direct alignment of cavities. In addition, the conservation of potentially druggable cavities varies among different proteins. In the comparison of multi- and single-chain IDPs, some multichain IDPs have an extremely high conservation, whereas another multichain IDPs' conservation appears worse, and the single-chain IDPs have relatively moderate conservations. This study is a new attempt to generally assess the potentially druggable cavities in IDPs for taking IDPs as druggable targets, and this work also lends support to the opinion of IDPs tending to bind to "multiconformational affinity" compounds.
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Affiliation(s)
- Bin Chong
- College of Chemistry and Molecular
Engineering, Center for Quantitative Biology, and Beijing National
Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China
| | - Maodong Li
- College of Chemistry and Molecular
Engineering, Center for Quantitative Biology, and Beijing National
Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China
| | - Tong Li
- Department
of Computer Science and Technology, Tsinghua
University, Beijing 100084, China
| | - Miao Yu
- College of Chemistry and Molecular
Engineering, Center for Quantitative Biology, and Beijing National
Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China
| | - Yugang Zhang
- Department
of Chemistry and Chemical Biology, Cornell
University, New York 14850, United States
| | - Zhirong Liu
- College of Chemistry and Molecular
Engineering, Center for Quantitative Biology, and Beijing National
Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing 100871, China
- E-mail: (Z.L.)
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27
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Ruan H, Sun Q, Zhang W, Liu Y, Lai L. Targeting intrinsically disordered proteins at the edge of chaos. Drug Discov Today 2018; 24:217-227. [PMID: 30278223 DOI: 10.1016/j.drudis.2018.09.017] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/16/2018] [Accepted: 09/26/2018] [Indexed: 12/20/2022]
Abstract
Intrinsically disordered proteins or intrinsically disordered regions (IDPs or IDRs) are those that do not fold into defined tertiary structures under physiological conditions. Given their prevalence in various diseases, IDPs are attractive therapeutic targets. However, because of the dynamic nature of the IDP structure, conventional structure-based drug design methods cannot be directly applied. Thanks to recent progress in understanding the mechanisms underlying IDP and ligand interactions, computational strategies for IDP-targeted rational drug discovery are emerging. Here, we summarize recent developments in computational IDP drug design strategies and their successful applications, analyze the typical properties of reported IDP-binding compounds (iIDPs), and discuss the major challenges ahead as well as possible solutions.
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Affiliation(s)
- Hao Ruan
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qi Sun
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Weilin Zhang
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ying Liu
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Luhua Lai
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Center for Quantitative Biology, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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28
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Schörghuber J, Geist L, Platzer G, Feichtinger M, Bisaccia M, Scheibelberger L, Weber F, Konrat R, Lichtenecker RJ. Late metabolic precursors for selective aromatic residue labeling. JOURNAL OF BIOMOLECULAR NMR 2018; 71:129-140. [PMID: 29808436 PMCID: PMC6096522 DOI: 10.1007/s10858-018-0188-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/19/2018] [Indexed: 06/08/2023]
Abstract
In recent years, we developed a toolbox of heavy isotope containing compounds, which serve as metabolic amino acid precursors in the E. coli-based overexpression of aromatic residue labeled proteins. Our labeling techniques show excellent results both in terms of selectivity and isotope incorporation levels. They are additionally distinguished by low sample production costs and meet the economic demands to further implement protein NMR spectroscopy as a routinely used method in drug development processes. Different isotopologues allow for the assembly of optimized protein samples, which fulfill the requirements of various NMR experiments to elucidate protein structures, analyze conformational dynamics, or probe interaction surfaces. In the present article, we want to summarize the precursors we developed so far and give examples of their special value in the probing of protein-ligand interaction.
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Affiliation(s)
- Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Leonhard Geist
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Gerald Platzer
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Michael Feichtinger
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Marilena Bisaccia
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Lukas Scheibelberger
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Frederik Weber
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology and Biotechnology, Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Dr-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Roman J Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria.
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29
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Currie SL, Lau DKW, Doane JJ, Whitby FG, Okon M, McIntosh LP, Graves BJ. Structured and disordered regions cooperatively mediate DNA-binding autoinhibition of ETS factors ETV1, ETV4 and ETV5. Nucleic Acids Res 2017; 45:2223-2241. [PMID: 28161714 PMCID: PMC5389675 DOI: 10.1093/nar/gkx068] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/29/2017] [Indexed: 12/21/2022] Open
Abstract
Autoinhibition enables spatial and temporal regulation of cellular processes by coupling protein activity to surrounding conditions, often via protein partnerships or signaling pathways. We report the molecular basis of DNA-binding autoinhibition of ETS transcription factors ETV1, ETV4 and ETV5, which are often overexpressed in prostate cancer. Inhibitory elements that cooperate to repress DNA binding were identified in regions N- and C-terminal of the ETS domain. Crystal structures of these three factors revealed an α-helix in the C-terminal inhibitory domain that packs against the ETS domain and perturbs the conformation of its DNA-recognition helix. Nuclear magnetic resonance spectroscopy demonstrated that the N-terminal inhibitory domain (NID) is intrinsically disordered, yet utilizes transient intramolecular interactions with the DNA-recognition helix of the ETS domain to mediate autoinhibition. Acetylation of selected lysines within the NID activates DNA binding. This investigation revealed a distinctive mechanism for DNA-binding autoinhibition in the ETV1/4/5 subfamily involving a network of intramolecular interactions not present in other ETS factors. These distinguishing inhibitory elements provide a platform through which cellular triggers, such as protein–protein interactions or post-translational modifications, may specifically regulate the function of these oncogenic proteins.
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Affiliation(s)
- Simon L Currie
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112-5550, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA
| | - Desmond K W Lau
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver BC, V6T 1Z3, Canada
| | - Jedediah J Doane
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112-5550, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA
| | - Frank G Whitby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver BC, V6T 1Z3, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver BC, V6T 1Z3, Canada
| | - Barbara J Graves
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112-5550, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
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30
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Oláh J, Bertrand P, Ovádi J. Role of the microtubule-associated TPPP/p25 in Parkinson's and related diseases and its therapeutic potential. Expert Rev Proteomics 2017; 14:301-309. [PMID: 28271739 DOI: 10.1080/14789450.2017.1304216] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The discovery and development of therapeutic strategies for the treatments of Parkinson's disease (PD) and other synucleinopathies are limited by a lack of understanding of the pathomechanisms and their connection with different diseases such as cancers. Areas covered: The hallmarks of these diseases are frequently multifunctional disordered proteins displaying moonlighting and/or chameleon features, which are challenging drug targets. A representative of these proteins is the disordered Tubulin Polymerization Promoting Protein (TPPP/p25) expressed specifically in oligodendrocytes (OLGs) in normal brain. Its non-physiological level is tightly related to the etiology of PD and Multiple System Atrophy (TPPP/p25 enrichment in inclusions of neurons and OLGs, respectively), multiple sclerosis (TPPP/p25-positive OLG destruction), as well as glioma (loss of TPPP/p25 expression). The established anti-proliferative potency of TPPP/p25 may raise its influence in cancer development. The recognition that whereas too much TPPP/p25 could kill neurons in PD, but its loss keeps cells alive in cancer could contribute to our understanding of the interrelationship of 'TPPP/p25 diseases'. Expert commentary: The knowledge accumulated so far underlines the key roles of the multifunctional TPPP/p25 in both physiological and diverse pathological processes, consequently its validation as drug target sorely needs a new innovative strategy that is briefly reviewed here.
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Affiliation(s)
- Judit Oláh
- a Institute of Enzymology , Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest , Hungary
| | - Philippe Bertrand
- b Institute of Chemistry for Materials and Medias, UMR CNRS 7285, University of Poitiers, 4 Rue Michel Brunet , TSA 51106 Poitiers cedex 9, France.,c REpiCGO network, Cancéropôle Grand Ouest, Maison de la Recherche en Santé, 63, quai Magellan 44000 Nantes , France
| | - Judit Ovádi
- a Institute of Enzymology , Research Centre for Natural Sciences, Hungarian Academy of Sciences , Budapest , Hungary
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Szénási T, Oláh J, Szabó A, Szunyogh S, Láng A, Perczel A, Lehotzky A, Uversky VN, Ovádi J. Challenging drug target for Parkinson's disease: Pathological complex of the chameleon TPPP/p25 and alpha-synuclein proteins. Biochim Biophys Acta Mol Basis Dis 2016; 1863:310-323. [PMID: 27671864 DOI: 10.1016/j.bbadis.2016.09.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/02/2016] [Accepted: 09/20/2016] [Indexed: 12/27/2022]
Abstract
The hallmarks of Parkinson's disease and other synucleinopathies, Tubulin Polymerization Promoting Protein (TPPP/p25) and α-synuclein (SYN) have two key features: they are disordered and co-enriched/co-localized in brain inclusions. These Neomorphic Moonlighting Proteins display both physiological and pathological functions due to their interactions with distinct partners. To achieve the selective targeting of the pathological TPPP/p25-SYN but not the physiological TPPP/p25-tubulin complex, their interfaces were identified as a specific innovative strategy for the development of anti-Parkinson drugs. Therefore, the interactions of TPPP/p25 with tubulin and SYN were characterized which suggested the involvements of the 178-187 aa and 147-156 aa segments in the complexation of TPPP/p25 with tubulin and SYN, respectively. However, various truncated and deletion mutants reduced but did not abolish the interactions except one mutant; in addition synthetized fragments corresponding to the potential binding segments of TPPP/p25 failed to interact with SYN. In fact, the studies of the multiple interactions at molecular and cellular levels revealed the high conformational plasticity, chameleon feature, of TPPP/p25 that ensures exceptional functional resilience; the lack of previously identified binding segments could be replaced by other segments. The experimental results are underlined by distinct bioinformatics tools. All these data revealed that although targeting chameleon proteins is a challenging task, nevertheless, the validation of a drug target can be achieved by identifying the interface of complexes of the partner proteins existing at the given pathological conditions.
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Affiliation(s)
- Tibor Szénási
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary.
| | - Judit Oláh
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary.
| | - Adél Szabó
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary.
| | - Sándor Szunyogh
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary.
| | - András Láng
- MTA-ELTE, Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Budapest 1117, Hungary.
| | - András Perczel
- MTA-ELTE, Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, Budapest 1117, Hungary; Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest 1117, Hungary.
| | - Attila Lehotzky
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 33612 Tampa, FL, USA; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.
| | - Judit Ovádi
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary.
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32
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Cao H, Huang Y, Liu Z. Interplay between binding affinity and kinetics in protein-protein interactions. Proteins 2016; 84:920-33. [PMID: 27018856 DOI: 10.1002/prot.25041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/24/2016] [Accepted: 03/17/2016] [Indexed: 12/18/2022]
Abstract
To clarify the interplay between the binding affinity and kinetics of protein-protein interactions, and the possible role of intrinsically disordered proteins in such interactions, molecular simulations were carried out on 20 protein complexes. With bias potential and reweighting techniques, the free energy profiles were obtained under physiological affinities, which showed that the bound-state valley is deep with a barrier height of 12 - 33 RT. From the dependence of the affinity on interface interactions, the entropic contribution to the binding affinity is approximated to be proportional to the interface area. The extracted dissociation rates based on the Arrhenius law correlate reasonably well with the experimental values (Pearson correlation coefficient R = 0.79). For each protein complex, a linear free energy relationship between binding affinity and the dissociation rate was confirmed, but the distribution of the slopes for intrinsically disordered proteins showed no essential difference with that observed for ordered proteins. A comparison with protein folding was also performed. Proteins 2016; 84:920-933. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Huaiqing Cao
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.,Center for Quantitative Biology, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, 100871, China
| | - Yongqi Huang
- Institute of Theoretical Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.,Center for Quantitative Biology, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, 100871, China
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33
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Structure-based Inhibitor Design for the Intrinsically Disordered Protein c-Myc. Sci Rep 2016; 6:22298. [PMID: 26931396 PMCID: PMC4773988 DOI: 10.1038/srep22298] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/11/2016] [Indexed: 12/19/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are associated with various diseases and have been proposed as promising drug targets. However, conventional structure-based approaches cannot be applied directly to IDPs, due to their lack of ordered structures. Here, we describe a novel computational approach to virtually screen for compounds that can simultaneously bind to different IDP conformations. The test system used c-Myc, an oncoprotein containing a disordered basic helix-loop-helix-leucine zipper (bHLH-LZ) domain that adopts a helical conformation upon binding to Myc-associated factor X (Max). For the virtual screen, we used three binding pockets in representative conformations of c-Myc370–409, which is part of the disordered bHLH-LZ domain. Seven compounds were found to directly bind c-Myc370–409in vitro, and four inhibited the growth of the c-Myc-overexpressing cells by affecting cell cycle progression. Our approach of IDP conformation sampling, binding site identification, and virtual screening for compounds that can bind to multiple conformations provides a useful strategy for structure-based drug discovery targeting IDPs.
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34
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Cino EA, Choy WY, Karttunen M. Characterization of the Free State Ensemble of the CoRNR Box Motif by Molecular Dynamics Simulations. J Phys Chem B 2016; 120:1060-8. [DOI: 10.1021/acs.jpcb.5b11565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Elio A. Cino
- Department
of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Wing-Yiu Choy
- Department
of Biochemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Mikko Karttunen
- Department of Mathematics and Computer Science & the Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, MetaForum, Eindhoven 5600 MB, The Netherlands
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35
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Li M, Liu Z. Dimensions, energetics, and denaturant effects of the protein unstructured state. Protein Sci 2016; 25:734-47. [PMID: 26683260 DOI: 10.1002/pro.2865] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/09/2015] [Accepted: 12/15/2015] [Indexed: 11/09/2022]
Abstract
Determining the energetics of the unfolded state of a protein is essential for understanding the folding mechanics of ordered proteins and the structure-function relation of intrinsically disordered proteins. Here, we adopt a coil-globule transition theory to develop a general scheme to extract interaction and free energy information from single-molecule fluorescence resonance energy transfer spectroscopy. By combining protein stability data, we have determined the free energy difference between the native state and the maximally collapsed denatured state in a number of systems, providing insight on the specific/nonspecific interactions in protein folding. Both the transfer and binding models of the denaturant effects are demonstrated to account for the revealed linear dependence of inter-residue interactions on the denaturant concentration, and are thus compatible under the coil-globule transition theory to further determine the dimension and free energy of the conformational ensemble of the unfolded state. The scaling behaviors and the effective θ-state are also discussed.
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Affiliation(s)
- Maodong Li
- College of Chemistry and Molecular Engineering, Center for Quantitative Biology, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, 100871, China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering, Center for Quantitative Biology, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, 100871, China
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36
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Wang F, Marshall CB, Ikura M. Forkhead followed by disordered tail: The intrinsically disordered regions of FOXO3a. INTRINSICALLY DISORDERED PROTEINS 2015; 3:e1056906. [PMID: 28232890 DOI: 10.1080/21690707.2015.1056906] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 05/22/2015] [Indexed: 12/22/2022]
Abstract
Forkhead box Class O is one of 19 subfamilies of the Forkhead box family, comprising 4 human transcription factors: FOXO1, FOXO3a, FOXO4, and FOXO6, which are involved in many crucial cellular processes. FOXO3a is a tumor suppressor involved in multiple physiological and pathological processes, and plays essential roles in metabolism, cell cycle arrest, DNA repair, and apoptosis. In its role as a transcription factor, the FOXO3a binds a consensus Forkhead response element DNA sequence, and recruits transcriptional coactivators to activate gene transcription. FOXO3a has additional functions, such as regulating p53-mediated apoptosis and activating kinase ATM. With the exception of the structured DNA-binding forkhead domain, most of the FOXO3a sequence comprises intrinsically disordered regions (IDRs), including 3 regions (CR1-3) that are conserved within the FOXO subfamily. Numerous studies have demonstrated that these IDRs directly mediate many of the diverse functions of FOXO3a. These regions contain post-translational modification and protein-protein interaction sites that integrate upstream signals to maintain homeostasis. Thus, the FOXO3a IDRs are emerging as key mediators of diverse regulatory processes, and represent an important target for the future development of therapeutics for FOXO3a-related diseases.
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Affiliation(s)
- Feng Wang
- The Campbell Family Cancer Research Institute, Princess Margaret Cancer Center, Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Present affiliation: Department of Biochemistry; Vanderbilt University School of Medicine; Nashville, TN USA
| | - Christopher B Marshall
- The Campbell Family Cancer Research Institute, Princess Margaret Cancer Center, Department of Medical Biophysics, University of Toronto , Toronto, Ontario, Canada
| | - Mitsuhiko Ikura
- The Campbell Family Cancer Research Institute, Princess Margaret Cancer Center, Department of Medical Biophysics, University of Toronto , Toronto, Ontario, Canada
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