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Del Val C, Díaz de la Guardia-Bolívar E, Zwir I, Mishra PP, Mesa A, Salas R, Poblete GF, de Erausquin G, Raitoharju E, Kähönen M, Raitakari O, Keltikangas-Järvinen L, Lehtimäki T, Cloninger CR. Gene expression networks regulated by human personality. Mol Psychiatry 2024:10.1038/s41380-024-02484-x. [PMID: 38433276 DOI: 10.1038/s41380-024-02484-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 03/05/2024]
Abstract
Genome-wide association studies of human personality have been carried out, but transcription of the whole genome has not been studied in relation to personality in humans. We collected genome-wide expression profiles of adults to characterize the regulation of expression and function in genes related to human personality. We devised an innovative multi-omic approach to network analysis to identify the key control elements and interactions in multi-modular networks. We identified sets of transcribed genes that were co-expressed in specific brain regions with genes known to be associated with personality. Then we identified the minimum networks for the co-localized genes using bioinformatic resources. Subjects were 459 adults from the Young Finns Study who completed the Temperament and Character Inventory and provided peripheral blood for genomic and transcriptomic analysis. We identified an extrinsic network of 45 regulatory genes from seed genes in brain regions involved in self-regulation of emotional reactivity to extracellular stimuli (e.g., self-regulation of anxiety) and an intrinsic network of 43 regulatory genes from seed genes in brain regions involved in self-regulation of interpretations of meaning (e.g., production of concepts and language). We discovered that interactions between the two networks were coordinated by a control hub of 3 miRNAs and 3 protein-coding genes shared by both. Interactions of the control hub with proteins and ncRNAs identified more than 100 genes that overlap directly with known personality-related genes and more than another 4000 genes that interact indirectly. We conclude that the six-gene hub is the crux of an integrative network that orchestrates information-transfer throughout a multi-modular system of over 4000 genes enriched in liquid-liquid-phase-separation (LLPS)-related RNAs, diverse transcription factors, and hominid-specific miRNAs and lncRNAs. Gene expression networks associated with human personality regulate neuronal plasticity, epigenesis, and adaptive functioning by the interactions of salience and meaning in self-awareness.
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Affiliation(s)
- Coral Del Val
- University of Granada, Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), Granada, Spain
| | - Elisa Díaz de la Guardia-Bolívar
- University of Granada, Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence, Granada, Spain
| | - Igor Zwir
- University of Granada, Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence, Granada, Spain
- Washington University School of Medicine, Department of Psychiatry, St. Louis, MO, USA
| | - Pashupati P Mishra
- Tampere University, Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Alberto Mesa
- University of Granada, Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence, Granada, Spain
| | - Ramiro Salas
- The Menninger Clinic, Baylor College of Medicine, and DeBakey VA Medical Center, Houston, TX, USA
| | | | - Gabriel de Erausquin
- University of Texas Health San Antonio, Long School of Medicine, Department of Neurology, Biggs Institute of Alzheimer's & Neurodegenerative Disorders, San Antonio, TX, USA
| | - Emma Raitoharju
- Tampere University, Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli Raitakari
- University of Turku and Turku University Hospital, Center for Population Health Research; University of Turku, Research Center of Applied and Preventive Cardiovascular Medicine; Turku University Hospital, Department of Clinical Physiology and Nuclear Medicine, Turku, Finland
| | | | - Terho Lehtimäki
- Tampere University, Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere, Finland
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2
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Narykov O, Zhu Y, Brettin T, Evrard YA, Partin A, Shukla M, Xia F, Clyde A, Vasanthakumari P, Doroshow JH, Stevens RL. Integration of Computational Docking into Anti-Cancer Drug Response Prediction Models. Cancers (Basel) 2023; 16:50. [PMID: 38201477 PMCID: PMC10777918 DOI: 10.3390/cancers16010050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 01/12/2024] Open
Abstract
Cancer is a heterogeneous disease in that tumors of the same histology type can respond differently to a treatment. Anti-cancer drug response prediction is of paramount importance for both drug development and patient treatment design. Although various computational methods and data have been used to develop drug response prediction models, it remains a challenging problem due to the complexities of cancer mechanisms and cancer-drug interactions. To better characterize the interaction between cancer and drugs, we investigate the feasibility of integrating computationally derived features of molecular mechanisms of action into prediction models. Specifically, we add docking scores of drug molecules and target proteins in combination with cancer gene expressions and molecular drug descriptors for building response models. The results demonstrate a marginal improvement in drug response prediction performance when adding docking scores as additional features, through tests on large drug screening data. We discuss the limitations of the current approach and provide the research community with a baseline dataset of the large-scale computational docking for anti-cancer drugs.
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Affiliation(s)
- Oleksandr Narykov
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (T.B.); (A.P.); (M.S.); (F.X.); (P.V.); (R.L.S.)
| | - Yitan Zhu
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (T.B.); (A.P.); (M.S.); (F.X.); (P.V.); (R.L.S.)
| | - Thomas Brettin
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (T.B.); (A.P.); (M.S.); (F.X.); (P.V.); (R.L.S.)
| | - Yvonne A. Evrard
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA;
| | - Alexander Partin
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (T.B.); (A.P.); (M.S.); (F.X.); (P.V.); (R.L.S.)
| | - Maulik Shukla
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (T.B.); (A.P.); (M.S.); (F.X.); (P.V.); (R.L.S.)
| | - Fangfang Xia
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (T.B.); (A.P.); (M.S.); (F.X.); (P.V.); (R.L.S.)
| | - Austin Clyde
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (T.B.); (A.P.); (M.S.); (F.X.); (P.V.); (R.L.S.)
- Department of Computer Science, The University of Chicago, Chicago, IL 60637, USA
| | - Priyanka Vasanthakumari
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (T.B.); (A.P.); (M.S.); (F.X.); (P.V.); (R.L.S.)
| | - James H. Doroshow
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA;
| | - Rick L. Stevens
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, IL 60439, USA; (Y.Z.); (T.B.); (A.P.); (M.S.); (F.X.); (P.V.); (R.L.S.)
- Department of Computer Science, The University of Chicago, Chicago, IL 60637, USA
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3
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Sarma H, Sastry GN. A Computational Study on the Interaction of NSP10 and NSP14: Unraveling the RNA Synthesis Proofreading Mechanism in SARS-CoV-2, SARS-CoV, and MERS-CoV. ACS OMEGA 2022; 7:30003-30022. [PMID: 36035077 PMCID: PMC9397572 DOI: 10.1021/acsomega.2c03007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
The interaction of exoribonuclease (ExoN) nonstructural protein (NSP14) with NSP10 co-factors is crucial for high-fidelity proofreading activity of coronavirus replication and transcription. Proofreading function is critical for maintaining the large genomes to ensure replication proficiency; therefore, while maintaining the viral replication fitness, quick resistance has been reported to the nucleotide analogue (NA) drugs. Therefore, targeting the NSP14 and NSP10 interacting interface with small molecules or peptides could be a better strategy to obstruct replication processes of coronaviruses (CoVs). A comparative study on the binding mechanism of NSP10 with the NSP14 ExoN domain of SARS-CoV-2, SARS-CoV, MERS-CoV, and four SARS-CoV-2 NSP14mutant complexes has been carried out. Protein-protein interaction (PPI) dynamics, per-residue binding free energy (BFE) analyses, and the identification of interface hotspot residues have been studied using molecular dynamics simulations and various computational tools. The BFE of the SARS-CoV NSP14-NSP10 complex was higher when compared to novel SARS-CoV-2 and MERS. However, SARS-CoV-2 NSP14mutant systems display a higher BFE as compared to the wild type (WT) but lower than SARS-CoV and MERS. Despite the high BFE, the SARS-CoV NSP14-NSP10 complex appears to be structurally more flexible in many regions especially the catalytic site, which is not seen in SARS-CoV-2 and its mutant or MERS complexes. The significantly high residue energy contribution of key interface residues and hotspots reveals that the high binding energy between NSP14 and NSP10 may enhance the functional activity of the proofreading complex, as the NSP10-NSP14 interaction is essential in maintaining the stability of the ExoN domain for the replicative fitness of CoVs. The factors discussed for SARS-CoV-2 complexes may be responsible for NSP14 ExoN having a high replication proficiency, significantly leading to the evolution of new variants of SARS-CoV-2. The NSP14 residues V66, T69, D126, and I201and eight residues of NSP10 (L16, F19, V21, V42, M44, H80, K93, and F96) are identified as common hotspots. Overall, the interface area, hotspot locations, bonded/nonbonded contacts, and energies between NSP14 and NSP10 may pave a way in designing potential inhibitors to disrupt NSP14-NSP10 interactions of CoVs especially SARS-CoV-2.
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Affiliation(s)
- Himakshi Sarma
- Advanced Computation and Data Sciences Division,
CSIR−North East Institute of Science and Technology,
Jorhat, Assam785006, India
| | - G. Narahari Sastry
- Advanced Computation and Data Sciences Division,
CSIR−North East Institute of Science and Technology,
Jorhat, Assam785006, India
- Academy of Scientific and Innovative
Research (AcSIR), Ghaziabad 201002, India
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4
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Taylor IR, Jeffrey PD, Moustafa DA, Goldberg JB, Bassler BL. The PqsE Active Site as a Target for Small Molecule Antimicrobial Agents against Pseudomonas aeruginosa. Biochemistry 2022; 61:1894-1903. [PMID: 35985643 PMCID: PMC9454246 DOI: 10.1021/acs.biochem.2c00334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
The opportunistic pathogen Pseudomonas
aeruginosa causes antibiotic-resistant, nosocomial
infections in immuno-compromised
individuals and is a high priority for antimicrobial development.
Key to pathogenicity in P. aeruginosa are biofilm formation and virulence factor production. Both traits
are controlled by the cell-to-cell communication process called quorum
sensing (QS). QS involves the synthesis, release, and population-wide
detection of signal molecules called autoinducers. We previously reported
that the activity of the RhlR QS transcription factor depends on a
protein–protein interaction with the hydrolase, PqsE, and PqsE
catalytic activity is dispensable for this interaction. Nonetheless,
the PqsE–RhlR interaction could be disrupted by the substitution
of an active site glutamate residue with tryptophan [PqsE(E182W)].
Here, we show that disruption of the PqsE–RhlR interaction
via either the E182W change or alteration of PqsE surface residues
that are essential for the interaction with RhlR attenuates P. aeruginosa infection in a murine host. We use
crystallography to characterize the conformational changes induced
by the PqsE(E182W) substitution to define the mechanism underlying
disruption of the PqsE–RhlR interaction. A loop rearrangement
that repositions the E280 residue in PqsE(E182W) is responsible for
the loss of interaction. We verify the implications garnered from
the PqsE(E182W) structure using mutagenic, biochemical, and additional
structural analyses. We present the next generation of molecules targeting
the PqsE active site, including a structure of the tightest binding
of these compounds, BB584, in complex with PqsE. The findings presented
here provide insights into drug discovery against P.
aeruginosa with PqsE as the target.
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Affiliation(s)
- Isabelle R Taylor
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Philip D Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Dina A Moustafa
- School of Medicine, Children's Healthcare of Atlanta, Inc., Department of Pediatrics, and Center for Cystic Fibrosis and Airway Diseases Research, Emory University, Atlanta, Georgia 30322, United States
| | - Joanna B Goldberg
- School of Medicine, Children's Healthcare of Atlanta, Inc., Department of Pediatrics, and Center for Cystic Fibrosis and Airway Diseases Research, Emory University, Atlanta, Georgia 30322, United States
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
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Sarma H, Jamir E, Sastry GN. Protein-protein interaction of RdRp with its co-factor NSP8 and NSP7 to decipher the interface hotspot residues for drug targeting: A comparison between SARS-CoV-2 and SARS-CoV. J Mol Struct 2022; 1257:132602. [PMID: 35153334 PMCID: PMC8824464 DOI: 10.1016/j.molstruc.2022.132602] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 02/09/2023]
Abstract
In this study we explored the molecular mechanism of RdRp (Non-Structural Protein, NSP12) interaction with its co-factors NSP7 and NSP8 which is the main toolbox for RNA replication and transcription of SARS-CoV-2 and SARS-CoV. The replication complex is a heterotetramer consists of one NSP12, one NSP7 and two NSP8. Extensive molecular dynamics (MD) simulations were applied on both the heterotetramer complexes to generate the conformations and were used to estimate the MMPBSA binding free energy (BFE) and per-residue energy decomposition of NSP12-NSP8 and NSP12-NSP7 and NSP7-NSP8 complexes. The BFE of SARS-CoV-2 heterotetramer complex with its corresponding partner protein was significantly higher as compared to SARS-CoV. Interface hotspot residues were predicted using different methods implemented in KFC (Knowledge-based FADA and Contracts), HotRegion and Robetta web servers. Per-residue energy decomposition analysis showed that the predicted interface hotspot residues contribute more energy towards the formation of complexes and most of the predicted hotspot residues are clustered together. However, there is a slight difference in the residue-wise energy contribution in the interface NSPs on heterotetramer viral replication complex of both coronaviruses. While the overall replication complex of SARS-CoV-2 was found to be slightly flexible as compared to SARS-CoV. This difference in terms of structural flexibility/stability and energetic characteristics of interface residues including hotspots at PPI interface in the viral replication complexes may be the reason of higher rate of RNA replication of SARS-CoV-2 as compared to SARS-CoV. Overall, the interaction profile at PPI interface such as, interface area, hotspot residues, nature of bonds and energies between NSPs, may provide valuable insights in designing of small molecules or peptide/peptidomimetic ligands which can fit into the PPI interface to disrupt the interaction.
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Affiliation(s)
- Himakshi Sarma
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, India
| | - Esther Jamir
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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6
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Farooq Z, Howell LA, McCormick PJ. Probing GPCR Dimerization Using Peptides. Front Endocrinol (Lausanne) 2022; 13:843770. [PMID: 35909575 PMCID: PMC9329873 DOI: 10.3389/fendo.2022.843770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of membrane proteins and the most common and extensively studied pharmacological target. Numerous studies over the last decade have confirmed that GPCRs do not only exist and function in their monomeric form but in fact, have the ability to form dimers or higher order oligomers with other GPCRs, as well as other classes of receptors. GPCR oligomers have become increasingly attractive to investigate as they have the ability to modulate the pharmacological responses of the receptors which in turn, could have important functional roles in diseases, such as cancer and several neurological & neuropsychiatric disorders. Despite the growing evidence in the field of GPCR oligomerisation, the lack of structural information, as well as targeting the 'undruggable' protein-protein interactions (PPIs) involved in these complexes, has presented difficulties. Outside the field of GPCRs, targeting PPIs has been widely studied, with a variety of techniques being investigated; from small-molecule inhibitors to disrupting peptides. In this review, we will demonstrate several physiologically relevant GPCR dimers and discuss an array of strategies and techniques that can be employed when targeting these complexes, as well as provide ideas for future development.
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Affiliation(s)
- Zara Farooq
- Centre for Endocrinology, William Harvey Research Institute, Bart’s and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, United Kingdom
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, Mile End Road, London, United Kingdom
| | - Lesley A. Howell
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, Mile End Road, London, United Kingdom
| | - Peter J. McCormick
- Centre for Endocrinology, William Harvey Research Institute, Bart’s and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, United Kingdom
- *Correspondence: Peter J. McCormick,
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7
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Rouhani M, Hadi-Alijanvand H. Effect of Lithium Drug on Binding Affinities of Glycogen Synthase Kinase-3 β to Its Network Partners: A New Computational Approach. J Chem Inf Model 2021; 61:5280-5292. [PMID: 34533953 DOI: 10.1021/acs.jcim.1c00952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Finding new methods to study the effect of small molecules on protein interaction networks provides us with invaluable tools in the fields of pharmacodynamics and drug design. Lithium is an antimanic drug that has been used for the treatment of bipolar disorder for more than 60 years. Here, we utilized a new approach to study the effect of lithium as a drug on the protein interaction network of GSK-3β as a hub protein and computed the affinities of GSK-3β to its partners in the presence of lithium or sodium ions. For this purpose, ensembles of GSK-3β protein structures were created in the presence of either lithium or sodium ions using adaptive tempering molecular dynamics simulations. The protein binding patches of GSK-3β for its partners were determined, and finally, the affinity of each binding patch to the related partner was computed for structures of ensembles using a monomer-based approach. Besides, by comparing structural dynamics of GSK-3β during MD simulations in the presence of LiCl and NaCl, we suggested a new mechanism for the inhibitory effect of lithium on GSK-3β.
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Affiliation(s)
- Maryam Rouhani
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Hamid Hadi-Alijanvand
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
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8
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Ajeeb B, Acar H, Detamore MS. Chondroinductive Peptides for Cartilage Regeneration. TISSUE ENGINEERING PART B-REVIEWS 2021; 28:745-765. [PMID: 34375146 DOI: 10.1089/ten.teb.2021.0125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Inducing and maintaining a hyaline cartilage phenotype is the greatest challenge for cartilage regeneration. Synthetic chondroinductive biomaterials might be the answer to the unmet clinical need for a safe, stable, and cost-effective material capable of inducing true hyaline cartilage formation. The past decade witnessed an emergence of peptides to achieve chondrogenesis, as peptides have the advantages of versatility, high target specificity, minimized toxicity and immunogenicity, and ease of synthesis. Here, we review peptides as the basis for creating promising synthetic chondroinductive biomaterials for in situ scaffold-based cartilage regeneration. We provide a thorough review of peptides evaluated for cartilage regeneration while distinguishing between peptides reported to induce chondrogenesis independently, and peptides reported to act in synergy with other growth factors to induce cartilage regeneration. Additionally, we highlight that most peptide studies have been in vitro, and appropriate controls are not always present. A few rigorously-performed in vitro studies have proceeded to in vivo studies, but the peptides in those in vivo studies were mainly introduced via systemic, subcutaneous, or intraarticular injections, with a paucity of studies employing in situ defects with appropriate controls. Clinical translation of peptides will require the evaluation of these peptides in well-controlled in vivo cartilage defect studies. In the decade ahead, we may be poised to leverage peptides to design devices that are safe, reproducible, cost-efficient, and scalable biomaterials, which are themselves chondroinductive to achieve true hyaline cartilage regeneration without the need for growth factors and other small molecules.
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Affiliation(s)
- Boushra Ajeeb
- University of Oklahoma, 6187, Biomedical Engineering, Norman, Oklahoma, United States;
| | - Handan Acar
- University of Oklahoma, 6187, Biomedical Engineering, Norman, Oklahoma, United States;
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9
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Shao H, Oltion K, Wu T, Gestwicki JE. Differential scanning fluorimetry (DSF) screen to identify inhibitors of Hsp60 protein-protein interactions. Org Biomol Chem 2021; 18:4157-4163. [PMID: 32458889 DOI: 10.1039/d0ob00928h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
There are relatively few methods available for discovering inhibitors of the protein-protein interactions (PPIs) that hold together homo-oligomers. We envisioned that Differential Scanning Fluorimetry (DSF) might be a versatile way to discover this type of inhibitor because oligomers are often more thermally stable than monomers. Using the homo-heptameric chaperonin, Hsp60, as a model, we screened ∼5000 diverse compounds in 384-well plates by DSF, revealing molecules that partially inhibited oligomerization. Because DSF does not require protein labeling or structural information, we propose that it could be a versatile way to uncover PPI inhibitors.
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Affiliation(s)
- Hao Shao
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Keely Oltion
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Taia Wu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
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10
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Perez JJ, Perez RA, Perez A. Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering. Front Mol Biosci 2021; 8:681617. [PMID: 34095231 PMCID: PMC8173110 DOI: 10.3389/fmolb.2021.681617] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/05/2021] [Indexed: 12/13/2022] Open
Abstract
Protein-protein interactions (PPIs) mediate a large number of important regulatory pathways. Their modulation represents an important strategy for discovering novel therapeutic agents. However, the features of PPI binding surfaces make the use of structure-based drug discovery methods very challenging. Among the diverse approaches used in the literature to tackle the problem, linear peptides have demonstrated to be a suitable methodology to discover PPI disruptors. Unfortunately, the poor pharmacokinetic properties of linear peptides prevent their direct use as drugs. However, they can be used as models to design enzyme resistant analogs including, cyclic peptides, peptide surrogates or peptidomimetics. Small molecules have a narrower set of targets they can bind to, but the screening technology based on virtual docking is robust and well tested, adding to the computational tools used to disrupt PPI. We review computational approaches used to understand and modulate PPI and highlight applications in a few case studies involved in physiological processes such as cell growth, apoptosis and intercellular communication.
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Affiliation(s)
- Juan J Perez
- Department of Chemical Engineering, Universitat Politecnica de Catalunya, Barcelona, Spain
| | - Roman A Perez
- Bioengineering Institute of Technology, Universitat Internacional de Catalunya, Sant Cugat, Spain
| | - Alberto Perez
- The Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, FL, United States
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11
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Serapian SA, Triveri A, Marchetti F, Castelli M, Colombo G. Exploiting Folding and Degradation Machineries To Target Undruggable Proteins: What Can a Computational Approach Tell Us? ChemMedChem 2021; 16:1593-1599. [PMID: 33443306 DOI: 10.1002/cmdc.202000960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Indexed: 01/03/2023]
Abstract
Advances in genomics and proteomics have unveiled an ever-growing number of key proteins and provided mechanistic insights into the genesis of pathologies. This wealth of data showed that changes in expression levels of specific proteins, mutations, and post-translational modifications can result in (often subtle) perturbations of functional protein-protein interaction networks, which ultimately determine disease phenotypes. Although many such validated pathogenic proteins have emerged as ideal drug targets, there are also several that escape traditional pharmacological regulation; these proteins have thus been labeled "undruggable". The challenges posed by undruggable targets call for new sorts of molecular intervention. One fascinating solution is to perturb a pathogenic protein's expression levels, rather than blocking its activities. In this Concept paper, we shall discuss chemical interventions aimed at recruiting undruggable proteins to the ubiquitin proteasome system, or aimed at disrupting protein-protein interactions in the chaperone-mediated cellular folding machinery: both kinds of intervention lead to a decrease in the amount of active pathogenic protein expressed. Specifically, we shall discuss the role of computational strategies in understanding the molecular determinants characterizing the function of synthetic molecules typically designed for either type of intervention. Finally, we shall provide our perspectives and views on the current limitations and possibilities to expand the scope of rational approaches to the design of chemical regulators of protein levels.
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Affiliation(s)
- Stefano A Serapian
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Alice Triveri
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Filippo Marchetti
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Matteo Castelli
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
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12
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Husain MA, Laurent B, Plourde M. APOE and Alzheimer's Disease: From Lipid Transport to Physiopathology and Therapeutics. Front Neurosci 2021; 15:630502. [PMID: 33679311 PMCID: PMC7925634 DOI: 10.3389/fnins.2021.630502] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/20/2021] [Indexed: 12/23/2022] Open
Abstract
Alzheimer’s disease (AD) is a devastating neurodegenerative disorder characterized by extracellular amyloid β (Aβ) and intraneuronal tau protein aggregations. One risk factor for developing AD is the APOE gene coding for the apolipoprotein E protein (apoE). Humans have three versions of APOE gene: ε2, ε3, and ε4 allele. Carrying the ε4 allele is an AD risk factor while carrying the ε2 allele is protective. ApoE is a component of lipoprotein particles in the plasma at the periphery, as well as in the cerebrospinal fluid (CSF) and in the interstitial fluid (ISF) of brain parenchyma in the central nervous system (CNS). ApoE is a major lipid transporter that plays a pivotal role in the development, maintenance, and repair of the CNS, and that regulates multiple important signaling pathways. This review will focus on the critical role of apoE in AD pathogenesis and some of the currently apoE-based therapeutics developed in the treatment of AD.
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Affiliation(s)
- Mohammed Amir Husain
- Centre de Recherche Sur le Vieillissement, Centre Intégré Universitaire de Santé et Services Sociaux de l'Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada.,Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Benoit Laurent
- Centre de Recherche Sur le Vieillissement, Centre Intégré Universitaire de Santé et Services Sociaux de l'Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada.,Département de Biochimie et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mélanie Plourde
- Centre de Recherche Sur le Vieillissement, Centre Intégré Universitaire de Santé et Services Sociaux de l'Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada.,Département de Médecine, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC, Canada
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13
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Cesa LC. Chemical Translational Biology: Redefining Druggability of Protein-Protein Interactions. Chembiochem 2020; 22:985-987. [PMID: 33205588 DOI: 10.1002/cbic.202000532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/14/2020] [Indexed: 11/10/2022]
Abstract
Chemical biologists use chemical tools to answer biological questions. The translational application of these principles has led to an explosion in the discovery and druggability of new protein targets, including protein-protein interactions (PPIs). Proteins tend to interact with other macromolecules using relatively large and featureless binding surfaces, which has hampered traditional drug discovery efforts, particularly for interactions with weaker affinity. In this article, I discuss several emerging strategies for targeting PPIs, including computational and structural methods and novel screening approaches. In particular, I focus on hijacking intrinsic protein allosteric pathways for the discovery and design of small-molecule and peptide ligands.
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Affiliation(s)
- Laura C Cesa
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
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14
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Nadel CM, Ran X, Gestwicki JE. Luminescence complementation assay for measurement of binding to protein C-termini in live cells. Anal Biochem 2020; 611:113947. [PMID: 32918866 DOI: 10.1016/j.ab.2020.113947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 11/28/2022]
Abstract
Protein-protein interactions (PPIs) involving the extreme C-terminus serve important scaffolding and regulatory functions. Here, we leveraged NanoBiT technology to build a luminescent complementation assay for use in studying this subcategory of PPI. As a model system, we fused one component of NanoBiT to the disordered C-terminus of heat shock protein (Hsp70) and the other to its binding partner, the tetratricopeptide repeat (TPR) domain of CHIP/STUB1. We found that HEK293 cells that stably express these chimeras under a doxycycline promoter produced a robust luminescence signal. This signal was sensitive to mutations and it was further tuned by the expression of competitive C-termini. Using this system, we identified a promising, membrane permeable inhibitor of the Hsp70-CHIP interaction. More broadly, we anticipate that NanoBiT is well-suited for studying PPIs that involve C-termini.
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Affiliation(s)
- Cory M Nadel
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Xu Ran
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA, 94158, USA.
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15
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Garlick JM, Mapp AK. Selective Modulation of Dynamic Protein Complexes. Cell Chem Biol 2020; 27:986-997. [PMID: 32783965 PMCID: PMC7469457 DOI: 10.1016/j.chembiol.2020.07.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/07/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022]
Abstract
Dynamic proteins perform critical roles in cellular machines, including those that control proteostasis, transcription, translation, and signaling. Thus, dynamic proteins are prime candidates for chemical probe and drug discovery but difficult targets because they do not conform to classical rules of design and screening. Selectivity is pivotal for candidate probe molecules due to the extensive interaction network of these dynamic hubs. Recognition that the traditional rules of probe discovery are not necessarily applicable to dynamic proteins and their complexes, as well as technological advances in screening, have produced remarkable results in the last 2-4 years. Particularly notable are the improvements in target selectivity for small-molecule modulators of dynamic proteins, especially with techniques that increase the discovery likelihood of allosteric regulatory mechanisms. We focus on approaches to small-molecule screening that appear to be more suitable for highly dynamic targets and have the potential to streamline identification of selective modulators.
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Affiliation(s)
- Julie M Garlick
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anna K Mapp
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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16
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Paladino A, Woodford MR, Backe SJ, Sager RA, Kancherla P, Daneshvar MA, Chen VZ, Bourboulia D, Ahanin EF, Prodromou C, Bergamaschi G, Strada A, Cretich M, Gori A, Veronesi M, Bandiera T, Vanna R, Bratslavsky G, Serapian SA, Mollapour M, Colombo G. Chemical Perturbation of Oncogenic Protein Folding: from the Prediction of Locally Unstable Structures to the Design of Disruptors of Hsp90-Client Interactions. Chemistry 2020; 26:9459-9465. [PMID: 32167602 PMCID: PMC7415569 DOI: 10.1002/chem.202000615] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Indexed: 12/20/2022]
Abstract
Protein folding quality control in cells requires the activity of a class of proteins known as molecular chaperones. Heat shock protein-90 (Hsp90), a multidomain ATP driven molecular machine, is a prime representative of this family of proteins. Interactions between Hsp90, its co-chaperones, and client proteins have been shown to be important in facilitating the correct folding and activation of clients. Hsp90 levels and functions are elevated in tumor cells. Here, we computationally predict the regions on the native structures of clients c-Abl, c-Src, Cdk4, B-Raf and Glucocorticoid Receptor, that have the highest probability of undergoing local unfolding, despite being ordered in their native structures. Such regions represent potential ideal interaction points with the Hsp90-system. We synthesize mimics spanning these regions and confirm their interaction with partners of the Hsp90 complex (Hsp90, Cdc37 and Aha1) by Nuclear Magnetic Resonance (NMR). Designed mimics selectively disrupt the association of their respective clients with the Hsp90 machinery, leaving unrelated clients unperturbed and causing apoptosis in cancer cells. Overall, selective targeting of Hsp90 protein-protein interactions is achieved without causing indiscriminate degradation of all clients, setting the stage for the development of therapeutics based on specific chaperone:client perturbation.
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Affiliation(s)
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Rebecca A Sager
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- College of Medicine, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Priyanka Kancherla
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Michael A Daneshvar
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Victor Z Chen
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Elham F Ahanin
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | | | | | | | | | | | - Marina Veronesi
- D3-PharmaChemistry, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Tiziano Bandiera
- D3-PharmaChemistry, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Renzo Vanna
- Institute for Photonics and Nanotechnologies, IFN-CNR, c/o Dept. of Physics, Politecnico di Milano, Piazza L. Da Vinci 32, 20133, Milano, Italy
| | - Gennady Bratslavsky
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Stefano A Serapian
- University of Pavia, Department of Chemistry, Viale Taramelli 10, 27100, Pavia, Italy
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Giorgio Colombo
- SCITEC-CNR, via Mario Bianco 9, 20131, Milano, Italy
- University of Pavia, Department of Chemistry, Viale Taramelli 10, 27100, Pavia, Italy
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17
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Serapian SA, Colombo G. Designing Molecular Spanners to Throw in the Protein Networks. Chemistry 2020; 26:4656-4670. [DOI: 10.1002/chem.201904523] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/18/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Stefano A. Serapian
- Department of ChemistryUniversity of Pavia Via Taramelli 12 27100 Pavia Italy
| | - Giorgio Colombo
- Department of ChemistryUniversity of Pavia Via Taramelli 12, 27 100 Pavia Italy
- SCITEC-CNR Via Mario Bianco 9 20131 Milano Italy
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18
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Williams T, Borchelt DR, Chakrabarty P. Therapeutic approaches targeting Apolipoprotein E function in Alzheimer's disease. Mol Neurodegener 2020; 15:8. [PMID: 32005122 PMCID: PMC6995170 DOI: 10.1186/s13024-020-0358-9] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
One of the primary genetic risk factors for Alzheimer’s disease (AD) is the presence of the Ɛ4 allele of apolipoprotein E (APOE). APOE is a polymorphic lipoprotein that is a major cholesterol carrier in the brain. It is also involved in various cellular functions such as neuronal signaling, neuroinflammation and glucose metabolism. Humans predominantly possess three different allelic variants of APOE, termed E2, E3, and E4, with the E3 allele being the most common. The presence of the E4 allele is associated with increased risk of AD whereas E2 reduces the risk. To understand the molecular mechanisms that underlie APOE-related genetic risk, considerable effort has been devoted towards developing cellular and animal models. Data from these models indicate that APOE4 exacerbates amyloid β plaque burden in a dose-dependent manner. and may also enhance tau pathogenesis in an isoform-dependent manner. Other studies have suggested APOE4 increases the risk of AD by mechanisms that are distinct from modulation of Aβ or tau pathology. Further, whether plasma APOE, by influencing systemic metabolic pathways, can also possibly alter CNS function indirectly is not complete;y understood. Collectively, the available studies suggest that APOE may impact multiple signaling pathways and thus investigators have sought therapeutics that would disrupt pathological functions of APOE while preserving or enhancing beneficial functions. This review will highlight some of the therapeutic strategies that are currently being pursued to target APOE4 towards preventing or treating AD and we will discuss additional strategies that holds promise for the future.
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Affiliation(s)
- Tosha Williams
- Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, 32610, USA.,Department of Neuroscience, University of Florida, Gainesville, FL, 32610, USA
| | - David R Borchelt
- Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, 32610, USA.,Department of Neuroscience, University of Florida, Gainesville, FL, 32610, USA.,McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Paramita Chakrabarty
- Center for Translational Research in Neurodegenerative Disease, University of Florida, Gainesville, FL, 32610, USA. .,Department of Neuroscience, University of Florida, Gainesville, FL, 32610, USA. .,McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
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19
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Covarrubias-Zambrano O, Yu J, Bossmann SH. Nano-Inspired Technologies for Peptide Delivery. Curr Protein Pept Sci 2019; 21:379-400. [PMID: 31793426 DOI: 10.2174/1389203720666191202112429] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/26/2019] [Accepted: 10/02/2019] [Indexed: 12/15/2022]
Abstract
Nano-inspired technologies offer unique opportunities to treat numerous diseases by using therapeutic peptides. Therapeutic peptides have attractive pharmacological profiles and can be manufactured at relatively low costs. The major advantages of using a nanodelivery approach comprises significantly lower required dosages compared to systemic delivery, and thus reduced toxicity and immunogenicity. The combination of therapeutic peptides with delivery peptides and nanoparticles or small molecule drugs offers systemic treatment approaches, instead of aiming for single biological targets or pathways. This review article discusses exemplary state-of-the-art nanosized delivery systems for therapeutic peptides and antibodies, as well as their biochemical and biophysical foundations and emphasizes still remaining challenges. The competition between using different nanoplatforms, such as liposome-, hydrogel-, polymer-, silica nanosphere-, or nanosponge-based delivery systems is still "on" and no clear frontrunner has emerged to date.
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Affiliation(s)
| | - Jing Yu
- Department of Chemistry, Kansas State University, 419 CBC Building, Manhattan, KS 66506-0401, United States.,Johns Hopkins University, Department of Radiology, Baltimore, MD, United States
| | - Stefan H Bossmann
- Department of Chemistry, Kansas State University, 419 CBC Building, Manhattan, KS 66506-0401, United States
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20
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Oyer HM, Sanders CM, Kim FJ. Small-Molecule Modulators of Sigma1 and Sigma2/TMEM97 in the Context of Cancer: Foundational Concepts and Emerging Themes. Front Pharmacol 2019; 10:1141. [PMID: 31695608 PMCID: PMC6816035 DOI: 10.3389/fphar.2019.01141] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/04/2019] [Indexed: 12/17/2022] Open
Abstract
There are two known subtypes of the so-called sigma receptors, Sigma1 and Sigma2. Sigma1 (encoded by the SIGMAR1 gene and also known as Sigma-1 receptor, S1R) is a unique pharmacologically regulated integral membrane chaperone or scaffolding protein that allosterically modulates the activity of its associated proteins. Sigma2, recently identified as transmembrane protein 97 (TMEM97), is an integral membrane protein implicated in cellular cholesterol homeostasis. A number of publications over the past two decades have suggested a role for both sigma proteins in tumor biology. Although there is currently no clinically used anti-cancer drug that targets Sigma1 or Sigma2/TMEM97, a growing body of evidence supports the potential of small-molecule compounds with affinity for these proteins, putative sigma ligands, as therapeutic agents to treat cancer. In preclinical models, these compounds have been reported to inhibit cancer cell proliferation, survival, adhesion, and migration; furthermore, they have been demonstrated to suppress tumor growth, to alleviate cancer-associated pain, and to exert immunomodulatory properties. Here, we will address the known knowns and the known unknowns of Sigma1 and Sigma2/TMEM97 ligand actions in the context of cancer. This review will highlight key discoveries and published evidence in support of a role for sigma proteins in cancer and will discuss several fundamental questions regarding the physiological roles of sigma proteins in cancer and sigma ligand mechanism of action.
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Affiliation(s)
- Halley M Oyer
- Department of Cancer Biology, Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, PA, United States
| | - Christina M Sanders
- Department of Cancer Biology, Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, PA, United States
| | - Felix J Kim
- Department of Cancer Biology, Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, PA, United States
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21
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Albert L, Peñalver A, Djokovic N, Werel L, Hoffarth M, Ruzic D, Xu J, Essen L, Nikolic K, Dou Y, Vázquez O. Modulating Protein–Protein Interactions with Visible‐Light‐Responsive Peptide Backbone Photoswitches. Chembiochem 2019; 20:1417-1429. [DOI: 10.1002/cbic.201800737] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Lea Albert
- Fachbereich ChemiePhilipps-Universität Marburg Hans-Meerwein-Strasse 4 35043 Marburg Germany
| | - Alberto Peñalver
- Fachbereich ChemiePhilipps-Universität Marburg Hans-Meerwein-Strasse 4 35043 Marburg Germany
| | - Nemanja Djokovic
- Department of Pharmaceutical ChemistryFaculty of PharmacyUniversity of Belgrade 450 Vojvode Stepe 11000 Belgrade Serbia
| | - Laura Werel
- Fachbereich ChemiePhilipps-Universität Marburg Hans-Meerwein-Strasse 4 35043 Marburg Germany
| | - Malte Hoffarth
- Fachbereich ChemiePhilipps-Universität Marburg Hans-Meerwein-Strasse 4 35043 Marburg Germany
| | - Dusan Ruzic
- Department of Pharmaceutical ChemistryFaculty of PharmacyUniversity of Belgrade 450 Vojvode Stepe 11000 Belgrade Serbia
| | - Jing Xu
- Department of PathologyUniversity of Michigan Ann Arbor MI 48109 USA
| | - Lars‐Oliver Essen
- Fachbereich ChemiePhilipps-Universität Marburg Hans-Meerwein-Strasse 4 35043 Marburg Germany
| | - Katarina Nikolic
- Department of Pharmaceutical ChemistryFaculty of PharmacyUniversity of Belgrade 450 Vojvode Stepe 11000 Belgrade Serbia
| | - Yali Dou
- Department of PathologyUniversity of Michigan Ann Arbor MI 48109 USA
| | - Olalla Vázquez
- Fachbereich ChemiePhilipps-Universität Marburg Hans-Meerwein-Strasse 4 35043 Marburg Germany
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22
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Joiner CM, Breen ME, Mapp AK. Electron-deficient p-benzoyl-l-phenylalanine derivatives increase covalent chemical capture yields for protein-protein interactions. Protein Sci 2019; 28:1163-1170. [PMID: 30977234 DOI: 10.1002/pro.3621] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/30/2022]
Abstract
The photoactivatable amino acid p-benzoyl-l-phenylalanine (pBpa) has been used for the covalent capture of protein-protein interactions (PPIs) in vitro and in living cells. However, this technique often suffers from poor photocrosslinking yields due to the low reactivity of the active species. Here we demonstrate that the incorporation of halogenated pBpa analogs into proteins leads to increased crosslinking yields for protein-protein interactions. The analogs can be incorporated into live yeast and upon irradiation capture endogenous PPIs. Halogenated pBpas will extend the scope of PPIs that can be captured and expand the toolbox for mapping PPIs in their native environment.
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Affiliation(s)
- Cassandra M Joiner
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Meghan E Breen
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Anna K Mapp
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan.,Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan
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23
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Ni D, Lu S, Zhang J. Emerging roles of allosteric modulators in the regulation of protein-protein interactions (PPIs): A new paradigm for PPI drug discovery. Med Res Rev 2019; 39:2314-2342. [PMID: 30957264 DOI: 10.1002/med.21585] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 03/12/2019] [Accepted: 03/24/2019] [Indexed: 12/26/2022]
Abstract
Protein-protein interactions (PPIs) are closely implicated in various types of cellular activities and are thus pivotal to health and disease states. Given their fundamental roles in a wide range of biological processes, the modulation of PPIs has enormous potential in drug discovery. However, owing to the general properties of large, flat, and featureless interfaces of PPIs, previous attempts have demonstrated that the generation of therapeutic agents targeting PPI interfaces is challenging, rendering them almost "undruggable" for decades. To date, rapid progress in chemical and structural biology techniques has promoted the exploitation of allostery as a novel approach in drug discovery. By attaching to allosteric sites that are topologically and spatially distinct from PPI interfaces, allosteric modulators can achieve improved physiochemical properties. Thus, allosteric modulators may represent an alternative strategy to target intractable PPIs and have attracted intense pharmaceutical interest. In this review, we first briefly introduce the characteristics of PPIs and then present different approaches for investigating PPIs, as well as the latest methods for modulating PPIs. Importantly, we comprehensively review the recent progress in the development of allosteric modulators to inhibit or stabilize PPIs. Finally, we conclude with future perspectives on the discovery of allosteric PPI modulators, especially the application of computational methods to aid in allosteric PPI drug discovery.
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Affiliation(s)
- Duan Ni
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Center for Single-Cell Omics, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
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24
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Rahimi MN, McAlpine SR. Protein-protein inhibitor designed de novo to target the MEEVD region on the C-terminus of Hsp90 and block co-chaperone activity. Chem Commun (Camb) 2019; 55:846-849. [PMID: 30575826 DOI: 10.1039/c8cc07576j] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein-protein interactions control all cellular functions. Presented is the first de novo designed protein-protein inhibitor that targets the C-terminus of heat shock protein 90 (Hsp90) and blocks co-chaperones from binding. Compound LB76, which was created from an Hsp90 co-chaperone, selectively pulls down Hsp90 from cell lysates, binds to Hsp90's C-terminal domain, and blocks the interactions between Hsp90 and TPR-containing co-chaperones. Through these interactions, LB76 inhibits the protein-folding function of Hsp90. Blocking these protein-protein interactions between Hsp90 and C-terminal co-chaperones regulate the cell's entire protein-folding machinery.
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Affiliation(s)
- Marwa N Rahimi
- School of Chemistry, Gate 2 High street, Dalton 219, University of New South Wales, Sydney, Australia.
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25
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Zaiter SS, Huo Y, Tiew FY, Gestwicki JE, McAlpine SR. Designing de Novo Small Molecules That Control Heat Shock Protein 70 (Hsp70) and Heat Shock Organizing Protein (HOP) within the Chaperone Protein-Folding Machinery. J Med Chem 2018; 62:742-761. [DOI: 10.1021/acs.jmedchem.8b01436] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Samantha S. Zaiter
- Department of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Yuantao Huo
- Department of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Fong Y. Tiew
- Department of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jason E. Gestwicki
- Department of Pharmaceutical Chemistry, Institute for Neuro-degenerative Disease, University of California, San Francisco, San Francisco, California 94158, United States
| | - Shelli R. McAlpine
- Department of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
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26
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Gestwicki JE, Shao H. Inhibitors and chemical probes for molecular chaperone networks. J Biol Chem 2018; 294:2151-2161. [PMID: 30213856 DOI: 10.1074/jbc.tm118.002813] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The molecular chaperones are central mediators of protein homeostasis. In that role, they engage in widespread protein-protein interactions (PPIs) with each other and with their "client" proteins. Together, these PPIs form the backbone of a network that ensures proper vigilance over the processes of protein folding, trafficking, quality control, and degradation. The core chaperones, such as the heat shock proteins Hsp60, Hsp70, and Hsp90, are widely expressed in most tissues, yet there is growing evidence that the PPIs among them may be re-wired in disease conditions. This possibility suggests that these PPIs, and perhaps not the individual chaperones themselves, could be compelling drug targets. Indeed, recent efforts have yielded small molecules that inhibit (or promote) a subset of inter-chaperone PPIs. These chemical probes are being used to study chaperone networks in a range of models, and the successes with these approaches have inspired a community-wide objective to produce inhibitors for a broader set of targets. In this Review, we discuss progress toward that goal and point out some of the challenges ahead.
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Affiliation(s)
- Jason E Gestwicki
- From the Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California 94158
| | - Hao Shao
- From the Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, California 94158
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27
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Ferraro M, Colombo G. Targeting Difficult Protein-Protein Interactions with Plain and General Computational Approaches. Molecules 2018; 23:molecules23092256. [PMID: 30181519 PMCID: PMC6225287 DOI: 10.3390/molecules23092256] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/27/2018] [Accepted: 08/31/2018] [Indexed: 11/21/2022] Open
Abstract
Investigating protein-protein interactions (PPIs) holds great potential for therapeutic applications, since they mediate intricate cell signaling networks in physiological and disease states. However, their complex and multifaceted nature poses a major challenge for biochemistry and medicinal chemistry, thereby limiting the druggability of biological partners participating in PPIs. Molecular Dynamics (MD) provides a solid framework to study the reciprocal shaping of proteins’ interacting surfaces. Here, we review successful applications of MD-based methods developed in our group to predict interfacial areas involved in PPIs of pharmaceutical interest. We report two interesting examples of how structural, dynamic and energetic information can be combined into efficient strategies which, complemented by experiments, can lead to the design of new small molecules with promising activities against cancer and infections. Our advances in targeting key PPIs in angiogenic pathways and antigen-antibody recognition events will be discussed for their role in drug discovery and chemical biology.
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Affiliation(s)
- Mariarosaria Ferraro
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy.
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy.
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
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28
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Che Y, Gilbert AM, Shanmugasundaram V, Noe MC. Inducing protein-protein interactions with molecular glues. Bioorg Med Chem Lett 2018; 28:2585-2592. [DOI: 10.1016/j.bmcl.2018.04.046] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/16/2018] [Accepted: 04/18/2018] [Indexed: 12/27/2022]
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29
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Ran X, Gestwicki JE. Inhibitors of protein-protein interactions (PPIs): an analysis of scaffold choices and buried surface area. Curr Opin Chem Biol 2018; 44:75-86. [PMID: 29908451 DOI: 10.1016/j.cbpa.2018.06.004] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/04/2018] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions (PPI) were once considered 'undruggable', but clinical successes, driven by advanced methods in drug discovery, have challenged that notion. Here, we review the last three years of literature on PPI inhibitors to understand what is working and why. From the 66 recently reported PPI inhibitors, we found that the average molecular weight was significantly greater than 500Da, but that this trend was driven, in large part, by the contribution of peptide-based compounds. Despite differences in average molecular weight, we found that compounds based on small molecules or peptides were almost equally likely to be potent inhibitors (KD<1μM). Finally, we found PPIs with buried surface area (BSA) less than 2000Å2 were more likely to be inhibited by small molecules, while PPIs with larger BSA values were typically inhibited by peptides. PPIs with BSA values over 4000Å2 seemed to create a particular challenge, especially for orthosteric small molecules. Thus, it seems important to choose the inhibitor scaffold based on the properties of the target interaction. Moreover, this survey suggests a (more nuanced) conclusion to the question of whether PPIs are good drug targets; namely, that some PPIs are readily 'druggable' given the right choice of scaffold, while others still seem to deserve the 'undruggable' moniker.
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Affiliation(s)
- Xu Ran
- Institute for Neurodegenerative Diseases and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, United States
| | - Jason E Gestwicki
- Institute for Neurodegenerative Diseases and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, United States.
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30
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Gee CT, Arntson KE, Koleski EJ, Staebell RL, Pomerantz WCK. Dual Labeling of the CBP/p300 KIX Domain for 19 F NMR Leads to Identification of a New Small-Molecule Binding Site. Chembiochem 2018; 19:963-969. [PMID: 29430847 PMCID: PMC6251716 DOI: 10.1002/cbic.201700686] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Indexed: 12/15/2022]
Abstract
Protein-Observed Fluorine NMR (PrOF NMR) spectroscopy is an emerging technique for screening and characterizing small-molecule-protein interactions. The choice of which amino acid to label for PrOF NMR can be critical for analysis. Here we report the first use of a protein containing two different fluoroaromatic amino acids for NMR studies. Using the KIX domain of the CBP/p300 as a model system, we examine ligand binding of several small-molecule compounds elaborated from our previous fragment screen and identify a new ligand binding site distinct from those used by native transcription factors. This site was further supported by computational modeling (FTMap and Schrödinger) and 1 H,15 N HSQC/HMQC NMR spectroscopy. Metabolic labeling with multiple fluorinated amino acids provides useful probes for further studying ligand binding and has led to new insight for allosterically regulating transcription-factor protein interactions with small-molecule ligands.
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Affiliation(s)
- Clifford T Gee
- Department of Chemistry, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, MN, 55455, USA
| | - Keith E Arntson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, MN, 55455, USA
| | - Edward J Koleski
- Department of Chemistry, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, MN, 55455, USA
| | - Rachel Lynn Staebell
- Department of Chemistry, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, MN, 55455, USA
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, MN, 55455, USA
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31
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Freilich R, Arhar T, Abrams JL, Gestwicki JE. Protein-Protein Interactions in the Molecular Chaperone Network. Acc Chem Res 2018; 51:940-949. [PMID: 29613769 DOI: 10.1021/acs.accounts.8b00036] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular chaperones play a central role in protein homeostasis (a.k.a. proteostasis) by balancing protein folding, quality control, and turnover. To perform these diverse tasks, chaperones need the malleability to bind nearly any "client" protein and the fidelity to detect when it is misfolded. Remarkably, these activities are carried out by only ∼180 dedicated chaperones in humans. How do a relatively small number of chaperones maintain cellular and organismal proteostasis for an entire proteome? Furthermore, once a chaperone binds a client, how does it "decide" what to do with it? One clue comes from observations that individual chaperones engage in protein-protein interactions (PPIs)-both with each other and with their clients. These physical links coordinate multiple chaperones into organized, functional complexes and facilitate the "handoff" of clients between them. PPIs also link chaperones and their clients to other cellular pathways, such as those that mediate trafficking (e.g., cytoskeleton) and degradation (e.g., proteasome). The PPIs of the chaperone network have a wide range of affinity values (nanomolar to micromolar) and involve many distinct types of domain modules, such as J domains, zinc fingers, and tetratricopeptide repeats. Many of these motifs have the same binding surfaces on shared partners, such that members of one chaperone class often compete for the same interactions. Somehow, this collection of PPIs draws together chaperone families and creates multiprotein subnetworks that are able to make the "decisions" of protein quality control. The key to understanding chaperone-mediated proteostasis might be to understand how PPIs are regulated. This Account will discuss the efforts of our group and others to map, measure, and chemically perturb the PPIs within the molecular chaperone network. Structural biology methods, including X-ray crystallography, NMR spectroscopy, and electron microscopy, have all played important roles in visualizing the chaperone PPIs. Guided by these efforts and -omics approaches to measure PPIs, new advances in high-throughput chemical screening that are specially designed to account for the challenges of this system have emerged. Indeed, chemical biology has played a particularly important role in this effort, as molecules that either promote or inhibit specific PPIs have proven to be invaluable research probes in cells and animals. In addition, these molecules have provided leads for the potential treatment of protein misfolding diseases. One of the major products of this research field has been the identification of putative PPI drug targets within the chaperone network, which might be used to change chaperone "decisions" and rebalance proteostasis.
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Affiliation(s)
- Rebecca Freilich
- Department of Pharmaceutical Chemistry and The Institute for Neurodegenerative Disease, University of California—San Francisco, San Francisco, California 94158, United States
| | - Taylor Arhar
- Department of Pharmaceutical Chemistry and The Institute for Neurodegenerative Disease, University of California—San Francisco, San Francisco, California 94158, United States
| | - Jennifer L. Abrams
- Department of Pharmaceutical Chemistry and The Institute for Neurodegenerative Disease, University of California—San Francisco, San Francisco, California 94158, United States
| | - Jason E. Gestwicki
- Department of Pharmaceutical Chemistry and The Institute for Neurodegenerative Disease, University of California—San Francisco, San Francisco, California 94158, United States
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32
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Acar H, Ting JM, Srivastava S, LaBelle JL, Tirrell MV. Molecular engineering solutions for therapeutic peptide delivery. Chem Soc Rev 2018; 46:6553-6569. [PMID: 28902203 DOI: 10.1039/c7cs00536a] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteins and their interactions in and out of cells must be well-orchestrated for the healthy functioning and regulation of the body. Even the slightest disharmony can cause diseases. Therapeutic peptides are short amino acid sequences (generally considered <50 amino acids) that can naturally mimic the binding interfaces between proteins and thus, influence protein-protein interactions. Because of their fidelity of binding, peptides are a promising next generation of personalized medicines to reinstate biological harmony. Peptides as a group are highly selective, relatively safe, and biocompatible. However, they are also vulnerable to many in vivo pharmacologic barriers limiting their clinical translation. Current advances in molecular, chemical, and nanoparticle engineering are helping to overcome these previously insurmountable obstacles and improve the future of peptides as active and highly selective therapeutics. In this review, we focus on self-assembled vehicles as nanoparticles to carry and protect therapeutic peptides through this journey, and deliver them to the desired tissue.
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Affiliation(s)
- Handan Acar
- Institute for Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
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33
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Taylor IR, Dunyak BM, Komiyama T, Shao H, Ran X, Assimon VA, Kalyanaraman C, Rauch JN, Jacobson MP, Zuiderweg ERP, Gestwicki JE. High-throughput screen for inhibitors of protein-protein interactions in a reconstituted heat shock protein 70 (Hsp70) complex. J Biol Chem 2018; 293:4014-4025. [PMID: 29414793 DOI: 10.1074/jbc.ra117.001575] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/22/2018] [Indexed: 12/15/2022] Open
Abstract
Protein-protein interactions (PPIs) are an important category of putative drug targets. Improvements in high-throughput screening (HTS) have significantly accelerated the discovery of inhibitors for some categories of PPIs. However, methods suitable for screening multiprotein complexes (e.g. those composed of three or more different components) have been slower to emerge. Here, we explored an approach that uses reconstituted multiprotein complexes (RMPCs). As a model system, we chose heat shock protein 70 (Hsp70), which is an ATP-dependent molecular chaperone that interacts with co-chaperones, including DnaJA2 and BAG2. The PPIs between Hsp70 and its co-chaperones stimulate nucleotide cycling. Thus, to re-create this ternary protein system, we combined purified human Hsp70 with DnaJA2 and BAG2 and then screened 100,000 diverse compounds for those that inhibited co-chaperone-stimulated ATPase activity. This HTS campaign yielded two compounds with promising inhibitory activity. Interestingly, one inhibited the PPI between Hsp70 and DnaJA2, whereas the other seemed to inhibit the Hsp70-BAG2 complex. Using secondary assays, we found that both compounds inhibited the PPIs through binding to allosteric sites on Hsp70, but neither affected Hsp70's intrinsic ATPase activity. Our RMPC approach expands the toolbox of biochemical HTS methods available for studying difficult-to-target PPIs in multiprotein complexes. The results may also provide a starting point for new chemical probes of the Hsp70 system.
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Affiliation(s)
- Isabelle R Taylor
- From the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 and
| | - Bryan M Dunyak
- From the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 and
| | - Tomoko Komiyama
- the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Hao Shao
- From the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 and
| | - Xu Ran
- From the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 and
| | - Victoria A Assimon
- From the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 and
| | - Chakrapani Kalyanaraman
- From the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 and
| | - Jennifer N Rauch
- From the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 and
| | - Matthew P Jacobson
- From the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 and
| | - Erik R P Zuiderweg
- the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Jason E Gestwicki
- From the Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 and
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34
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Rivera-Sánchez MC, García-Arriaga M, Hobley G, Morales-de-Echegaray AV, Rivera JM. Small-Molecule-Based Self-Assembled Ligands for G-Quadruplex DNA Surface Recognition. ACS OMEGA 2017; 2:6619-6627. [PMID: 29104952 PMCID: PMC5664172 DOI: 10.1021/acsomega.7b01255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 09/27/2017] [Indexed: 05/08/2023]
Abstract
Most drugs are small molecules because of their attractive pharmacokinetics, manageable development and manufacturing, and effective binding into the concave crevices of bio-macromolecules. Despite these features, they often fall short when it comes to effectively recognizing the surfaces of bio-macromolecules. One way to overcome the challenge of biomolecular surface recognition is to develop small molecules that become self-assembled ligands (SALs) prior to binding. Herein, we report SALs made from 8-aryl-2'-deoxyguanosine derivatives forming precise hydrophilic supramolecular G-quadruplexes (SGQs) with excellent size, shape, and charge complementarity to G-quadruplex DNA (QDNA). We show that only those compounds forming SGQs act as SALs, which in turn differentially stabilize QDNAs from selected oncogene promoters and the human telomeric regions. Fluorescence resonance energy-transfer melting assays are consistent with spectroscopic, calorimetric, and light scattering studies, showing the formation of a "sandwichlike" complex QDNA·SGQ·QDNA. These results open the door for the advent of SALs that recognize QDNAs and potentially the surfaces of other bio-macromolecules such as proteins.
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Affiliation(s)
- María
del C. Rivera-Sánchez
- Department of Chemistry and
Molecular Sciences Research Center, University
of Puerto Rico at Río Piedras, San Juan, Puerto Rico 00926, United States
| | - Marilyn García-Arriaga
- Department of Chemistry and
Molecular Sciences Research Center, University
of Puerto Rico at Río Piedras, San Juan, Puerto Rico 00926, United States
| | - Gerard Hobley
- Department of Chemistry and
Molecular Sciences Research Center, University
of Puerto Rico at Río Piedras, San Juan, Puerto Rico 00926, United States
| | - Ana V. Morales-de-Echegaray
- Department of Chemistry and
Molecular Sciences Research Center, University
of Puerto Rico at Río Piedras, San Juan, Puerto Rico 00926, United States
| | - José M. Rivera
- Department of Chemistry and
Molecular Sciences Research Center, University
of Puerto Rico at Río Piedras, San Juan, Puerto Rico 00926, United States
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35
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van Dun S, Ottmann C, Milroy LG, Brunsveld L. Supramolecular Chemistry Targeting Proteins. J Am Chem Soc 2017; 139:13960-13968. [PMID: 28926241 PMCID: PMC5639466 DOI: 10.1021/jacs.7b01979] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Indexed: 12/19/2022]
Abstract
The specific recognition of protein surface elements is a fundamental challenge in the life sciences. New developments in this field will form the basis of advanced therapeutic approaches and lead to applications such as sensors, affinity tags, immobilization techniques, and protein-based materials. Synthetic supramolecular molecules and materials are creating new opportunities for protein recognition that are orthogonal to classical small molecule and protein-based approaches. As outlined here, their unique molecular features enable the recognition of amino acids, peptides, and even whole protein surfaces, which can be applied to the modulation and assembly of proteins. We believe that structural insights into these processes are of great value for the further development of this field and have therefore focused this Perspective on contributions that provide such structural data.
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Affiliation(s)
- Sam van Dun
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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36
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Pricer R, Gestwicki JE, Mapp AK. From Fuzzy to Function: The New Frontier of Protein-Protein Interactions. Acc Chem Res 2017; 50:584-589. [PMID: 28945413 DOI: 10.1021/acs.accounts.6b00565] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Conformationally heterogenous or "fuzzy" proteins have often been described as lacking specificity in binding and in function. The activation domains, for example, of transcriptional activators were labeled as negative noodles, with little structure or specificity. However, emerging data illustrates that the opposite is true: conformational heterogeneity enables context-specific function to emerge in response to changing cellular conditions and, furthermore, allows a single structural motif to be used in multiple settings. A further benefit is that conformational heterogeneity can be harnessed for the discovery of allosteric drug-like modulators, targeting critical pathways in protein homeostasis and transcription.
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Affiliation(s)
- Rachel Pricer
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109-2216, United States
- Program
in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109-2216, United States
| | - Jason E Gestwicki
- Institute
for Neurodegenerative Diseases, Department of Pharmaceutical Chemistry, University of California—San Francisco, San Francisco, California 94143-0518, United States
| | - Anna K Mapp
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109-2216, United States
- Program
in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109-2216, United States
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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37
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Abstract
Sigma1 (also known as sigma-1 receptor, Sig1R, σ1 receptor) is a unique pharmacologically regulated integral membrane chaperone or scaffolding protein. The majority of publications on the subject have focused on the neuropharmacology of Sigma1. However, a number of publications have also suggested a role for Sigma1 in cancer. Although there is currently no clinically used anti-cancer drug that targets Sigma1, a growing body of evidence supports the potential of Sigma1 ligands as therapeutic agents to treat cancer. In preclinical models, compounds with affinity for Sigma1 have been reported to inhibit cancer cell proliferation and survival, cell adhesion and migration, tumor growth, to alleviate cancer-associated pain, and to have immunomodulatory properties. This review will highlight that although the literature supports a role for Sigma1 in cancer, several fundamental questions regarding drug mechanism of action and the physiological relevance of aberrant SIGMAR1 transcript and Sigma1 protein expression in certain cancers remain unanswered or only partially answered. However, emerging lines of evidence suggest that Sigma1 is a component of the cancer cell support machinery, that it facilitates protein interaction networks, that it allosterically modulates the activity of its associated proteins, and that Sigma1 is a selectively multifunctional drug target.
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Affiliation(s)
- Felix J Kim
- Department of Pharmacology and Physiology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA, USA.
- Sidney Kimmel Cancer Center, Philadelphia, PA, USA.
| | - Christina M Maher
- Department of Pharmacology and Physiology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA, USA
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38
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Brobeil A, Dietel E, Gattenlöhner S, Wimmer M. Orchestrating cellular signaling pathways-the cellular "conductor" protein tyrosine phosphatase interacting protein 51 (PTPIP51). Cell Tissue Res 2016; 368:411-423. [PMID: 27734150 DOI: 10.1007/s00441-016-2508-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/07/2016] [Indexed: 12/28/2022]
Abstract
The protein tyrosine phosphatase interacting protein 51 (PTPIP51) is thought to regulate crucial cellular functions such as mitosis, apoptosis, migration, differentiation and communication between organelles as a scaffold protein. These diverse functions are modulated by the tyrosine/serine phosphorylation status of PTPIP51. This review interconnects the insights obtained about the action of PTPIP51 in mitogen-activated protein kinase signaling, nuclear factor kB signaling, calcium homeostasis and chromosomal segregation and identifies important signaling hubs. The interference of PTPIP51 in such multiprotein complexes and their PTPIP51-modulated cross-talk makes PTPIP51 an ideal target for novel drugs such as the small molecule LDC-3. Graphical Abstract ᅟ.
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Affiliation(s)
- Alexander Brobeil
- Institute of Anatomy and Cell Biology, Justus-Liebig-University, 35392, Giessen, Germany. .,Institute of Pathology, Justus-Liebig-University, 35392, Giessen, Germany.
| | - Eric Dietel
- Institute of Anatomy and Cell Biology, Justus-Liebig-University, 35392, Giessen, Germany
| | | | - Monika Wimmer
- Institute of Anatomy and Cell Biology, Justus-Liebig-University, 35392, Giessen, Germany
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39
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Dunyak BM, Gestwicki JE. Peptidyl-Proline Isomerases (PPIases): Targets for Natural Products and Natural Product-Inspired Compounds. J Med Chem 2016; 59:9622-9644. [PMID: 27409354 DOI: 10.1021/acs.jmedchem.6b00411] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peptidyl-proline isomerases (PPIases) are a chaperone superfamily comprising the FK506-binding proteins (FKBPs), cyclophilins, and parvulins. PPIases catalyze the cis/trans isomerization of proline, acting as a regulatory switch during folding, activation, and/or degradation of many proteins. These "clients" include proteins with key roles in cancer, neurodegeneration, and psychiatric disorders, suggesting that PPIase inhibitors could be important therapeutics. However, the active site of PPIases is shallow, solvent-exposed, and well conserved between family members, making selective inhibitor design challenging. Despite these hurdles, macrocyclic natural products, including FK506, rapamycin, and cyclosporin, bind PPIases with nanomolar or better affinity. De novo attempts to derive new classes of inhibitors have been somewhat less successful, often showcasing the "undruggable" features of PPIases. Interestingly, the most potent of these next-generation molecules tend to integrate features of the natural products, including macrocyclization or proline mimicry strategies. Here, we review recent developments and ongoing challenges in the inhibition of PPIases, with a focus on how natural products might inform the creation of potent and selective inhibitors.
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Affiliation(s)
- Bryan M Dunyak
- Department of Biological Chemistry, University of Michigan Medical School , 1150 W. Medical Center Drive, Ann Arbor, Michigan 48109, United States.,Department of Pharmaceutical Chemistry, University of California at San Francisco , 675 Nelson Rising Lane, San Francisco, California 94158, United States
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California at San Francisco , 675 Nelson Rising Lane, San Francisco, California 94158, United States
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40
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Kampinga HH, Bergink S. Heat shock proteins as potential targets for protective strategies in neurodegeneration. Lancet Neurol 2016; 15:748-759. [PMID: 27106072 DOI: 10.1016/s1474-4422(16)00099-5] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/09/2016] [Accepted: 02/24/2016] [Indexed: 01/08/2023]
Abstract
Protein aggregates are hallmarks of nearly all age-related neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and several polyglutamine diseases such as Huntington's disease and different forms of spinocerebellar ataxias (SCA; SCA1-3, SCA6, and SCA7). The collapse of cellular protein homoeostasis can be both a cause and a consequence of this protein aggregation. Boosting components of the cellular protein quality control system has been widely investigated as a strategy to counteract protein aggregates or their toxic consequences. Heat shock proteins (HSPs) play a central part in regulating protein quality control and contribute to protein aggregation and disaggregation. Therefore, HSPs are viable targets for the development of drugs aimed at reducing pathogenic protein aggregates that are thought to contribute to the development of so many neurodegenerative disorders.
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Affiliation(s)
- Harm H Kampinga
- Department of Cell Biology, University Medical Center Groningen, Rijksuniversiteit Groningen, Groningen, Netherlands.
| | - Steven Bergink
- Department of Cell Biology, University Medical Center Groningen, Rijksuniversiteit Groningen, Groningen, Netherlands
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41
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Mapp AK, Pricer R, Sturlis S. Targeting transcription is no longer a quixotic quest. Nat Chem Biol 2016; 11:891-4. [PMID: 26575226 DOI: 10.1038/nchembio.1962] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Anna K Mapp
- Life Sciences Institute and the Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Rachel Pricer
- Life Sciences Institute and the Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Steven Sturlis
- Life Sciences Institute and the Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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