201
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Gilberg E, Stumpfe D, Bajorath J. X-ray-Structure-Based Identification of Compounds with Activity against Targets from Different Families and Generation of Templates for Multitarget Ligand Design. ACS OMEGA 2018; 3:106-111. [PMID: 30023769 PMCID: PMC6045467 DOI: 10.1021/acsomega.7b01849] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/18/2017] [Indexed: 05/22/2023]
Abstract
Compounds with multitarget activity (promiscuity) are increasingly sought in drug discovery. However, promiscuous compounds are often viewed controversially in light of potential assay artifacts that may give rise to false-positive activity annotations. We have reasoned that the strongest evidence for true multitarget activity of small molecules would be provided by experimentally determined structures of ligand-target complexes. Therefore, we have carried out a systematic search of currently available X-ray structures for compounds forming complexes with different targets. Rather unexpectedly, 1418 such crystallographic ligands were identified, including 702 that formed complexes with targets from different protein families (multifamily ligands). About half of these multifamily ligands originated from the medicinal chemistry literature, making it possible to consider additional target annotations and search for analogues. From 168 distinct series of analogues containing one or more multifamily ligands, 133 unique analogue-series-based scaffolds were isolated that can serve as templates for the design of new compounds with multitarget activity. As a part of our study, all of the multifamily ligands we have identified and the analogue-series-based scaffolds are made freely available.
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Affiliation(s)
- Erik Gilberg
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
- Pharmaceutical
Institute, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 4, D-53121 Bonn, Germany
| | - Dagmar Stumpfe
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
| | - Jürgen Bajorath
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
- Phone: 49-228-2699-306. E-mail:
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202
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Gilberg E, Gütschow M, Bajorath J. X-ray Structures of Target–Ligand Complexes Containing Compounds with Assay Interference Potential. J Med Chem 2018; 61:1276-1284. [DOI: 10.1021/acs.jmedchem.7b01780] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Erik Gilberg
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
- Pharmaceutical
Institute, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 4, D-53121 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical
Institute, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 4, D-53121 Bonn, Germany
| | - Jürgen Bajorath
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
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203
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Vickery CR, Wood BM, Morris HG, Losick R, Walker S. Reconstitution of Staphylococcus aureus Lipoteichoic Acid Synthase Activity Identifies Congo Red as a Selective Inhibitor. J Am Chem Soc 2018; 140:876-879. [PMID: 29300473 PMCID: PMC5856125 DOI: 10.1021/jacs.7b11704] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Lipoteichoic acid (LTA) is an anionic surface polymer that is essential for normal growth of Staphylococcus aureus, making the LTA polymerase, LTA synthase (LtaS), a proposed drug target for combating Staphylococcal infections. LtaS is a polytopic membrane protein with five membrane-spanning helices and an extracellular domain, and it uses phosphatidylglycerol to assemble a glycerol phosphate chain on a glycosylated diacylglycerol membrane anchor. We report here the first reconstitution of LtaS polymerization activity and show that the azo dye Congo red inhibits this enzyme both in vitro and in cells. Related azo dyes and the previously reported LtaS inhibitor 1771 have weak or no in vitro inhibitory activity. Synthetic lethality with mutant strains known to be nonviable in the absence of LTA confirms selective inhibition by Congo red. As the only validated LtaS inhibitor, Congo red can serve as a probe to understand how inhibiting lipoteichoic acid biosynthesis affects cell physiology and may also guide the discovery of more potent inhibitors for use in treating S. aureus infections.
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Affiliation(s)
- Christopher R. Vickery
- Department of Microbiology and Immunobiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - B. McKay Wood
- Department of Microbiology and Immunobiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Heidi G. Morris
- Department of Microbiology and Immunobiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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204
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Kolte BS, Londhe SR, Solanki BR, Gacche RN, Meshram RJ. FilTer BaSe: A web accessible chemical database for small compound libraries. J Mol Graph Model 2018; 80:95-103. [PMID: 29328995 DOI: 10.1016/j.jmgm.2017.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 12/22/2017] [Accepted: 12/28/2017] [Indexed: 12/11/2022]
Abstract
Finding novel chemical agents for targeting disease associated drug targets often requires screening of large number of new chemical libraries. In silico methods are generally implemented at initial stages for virtual screening. Filtering of such compound libraries on physicochemical and substructure ground is done to ensure elimination of compounds with undesired chemical properties. Filtering procedure, is redundant, time consuming and requires efficient bioinformatics/computer manpower along with high end software involving huge capital investment that forms a major obstacle in drug discovery projects in academic setup. We present an open source resource, FilTer BaSe- a chemoinformatics platform (http://bioinfo.net.in/filterbase/) that host fully filtered, ready to use compound libraries with workable size. The resource also hosts a database that enables efficient searching the chemical space of around 348,000 compounds on the basis of physicochemical and substructure properties. Ready to use compound libraries and database presented here is expected to aid a helping hand for new drug developers and medicinal chemists.
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Affiliation(s)
- Baban S Kolte
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, 411007, India
| | - Sanjay R Londhe
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, 411007, India
| | | | - Rajesh N Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, 411007, India
| | - Rohan J Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, 411007, India.
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205
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Series of screening compounds with high hit rates for the exploration of multi-target activities and assay interference. Future Sci OA 2018; 4:FSO279. [PMID: 29568568 PMCID: PMC5861374 DOI: 10.4155/fsoa-2017-0137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 12/13/2017] [Indexed: 12/02/2022] Open
Abstract
Aim: Generation of a database of analog series (ASs) with high assay hit rates for the exploration of assay interference and multi-target activities of compounds. Methodology: ASs were computationally extracted from extensively tested screening compounds with high hit rates. Data: A total of 6941 ASs were assembled comprising 14,646 unique compounds that were tested in a total of 1241 different assays covering 426 specified targets. These ASs were organized and prioritized on the basis of different activity and assay frequency criteria. All ASs and associated information are made available in an open access deposition. Next steps: The large set of ASs will be further analyzed computationally and from a chemical perspective to identify assay interference compounds and candidates for exploring target promiscuity. In drug discovery, compounds are tested in high-throughput screening assays for desired biological activities. Unfortunately, some test compounds that are not specifically active give false-positive (artificial) activity signals in assays, which are difficult to recognize. However, other compounds can bind specifically to multiple targets and hence give true activity signals in multiple assays. To help distinguish between artifacts and true activities, we have systematically identified series of analogs (i.e., structurally closely related compounds) that are active with unusually high frequency across biological assays. Herein, we describe these data and make them freely available for follow-up analysis.
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206
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207
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208
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Brender JR, Krishnamoorthy J, Ghosh A, Bhunia A. Binding Moiety Mapping by Saturation Transfer Difference NMR. Methods Mol Biol 2018; 1824:49-65. [PMID: 30039401 DOI: 10.1007/978-1-4939-8630-9_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Saturation transfer difference (STD) NMR has emerged as one of the key technologies in lead optimization during drug design. Unlike most biophysical assays which report only on the binding affinity, STD NMR reports simultaneously on both the binding affinity and the structure of the binding ligand/protein complex. The STD experiment drives magnetization from a protein to a bound small molecule ligand which carries away the memory of the saturation signal when it dissociates. Since the transfer of saturation is distance dependent, STD NMR can be used to map the specific atoms on the ligand in contact with a protein receptor allowing the impact of any structural change in the binding site to be mapped directly on to the individual functional groups responsible when a suitable compound library is screened. Because the signal is detected from the free ligand and not the bound complex, it can be used on a much wider range of systems than protein-detected NMR and has the advantage of more directly reporting on distances than changes in chemical shifts alone. The STD experiment, while deceptively simple, is very sensitive to both sample conditions and acquisition parameters. We present a general protocol for setting up and STD NMR experiment with a particular focus on how choices in sample conditions and acquisition parameters affect the outcome of the experiment.
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Affiliation(s)
- Jeffrey R Brender
- Radiation Biology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | | | - Anirban Ghosh
- Department of Biophysics, Bose Institute, Kolkata, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, India
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209
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Abstract
Over the past few decades, NMR spectroscopy has become an established tool in drug discovery. This communication will highlight the potential of NMR spectroscopy as a method for identification of problematic compounds and as a valuable aid toward revealing some mechanisms of promiscuous behavior. NMR methods for detecting false positives will be analyzed on the basis of their performance, strengths, limitations, and potential pitfalls. Additionally, this communication aims to provide an insight into the limitations of NMR-based methodologies applied to ligand screening in the context of false-positive hits.
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Affiliation(s)
- Anamarija Zega
- Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia
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210
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Song JM, Menon A, Mitchell DC, Johnson OT, Garner AL. High-Throughput Chemical Probing of Full-Length Protein-Protein Interactions. ACS COMBINATORIAL SCIENCE 2017; 19:763-769. [PMID: 29112379 PMCID: PMC5939945 DOI: 10.1021/acscombsci.7b00128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human biology is regulated by a complex network of protein-protein interactions (PPIs), and disruption of this network has been implicated in many diseases. However, the targeting of PPIs remains a challenging area for chemical probe and drug discovery. Although many methodologies have been put forth to facilitate these efforts, new technologies are still needed. Current biochemical assays for PPIs are typically limited to motif-domain and domain-domain interactions, and assays that will enable the screening of full-length protein systems, which are more biologically relevant, are sparse. To overcome this barrier, we have developed a new assay technology, "PPI catalytic enzyme-linked click chemistry assay" or PPI cat-ELCCA, which utilizes click chemistry to afford catalytic signal amplification. To validate this approach, we have applied PPI cat-ELCCA to the eIF4E-4E-BP1 and eIF4E-eIF4G PPIs, key regulators of cap-dependent mRNA translation. Using these examples, we have demonstrated that PPI cat-ELCCA is amenable to full-length proteins, large (>200 kDa) and small (∼12 kDa), and is readily adaptable to automated high-throughput screening. Thus, PPI cat-ELCCA represents a powerful new tool in the toolbox of assays available to scientists interested in the targeting of disease-relevant PPIs.
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Affiliation(s)
- James M. Song
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Arya Menon
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dylan C. Mitchell
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Oleta T. Johnson
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amanda L. Garner
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
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211
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A multifaceted approach to identify non-specific enzyme inhibition: Application to Mycobacterium tuberculosis shikimate kinase. Bioorg Med Chem Lett 2017; 28:802-808. [PMID: 29366649 DOI: 10.1016/j.bmcl.2017.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/29/2017] [Accepted: 12/01/2017] [Indexed: 12/13/2022]
Abstract
Single dose high-throughput screening (HTS) followed by dose-response evaluations is a common strategy for the identification of initial hits for further development. Early identification and exclusion of false positives is a cost-saving and essential step in early drug discovery. One of the mechanisms of false positive compounds is the formation of aggregates in assays. This study evaluates the mechanism(s) of inhibition of a set of 14 compounds identified previously as actives in Mycobacterium tuberculosis (Mt) cell culture screening and in vitro actives in Mt shikimate kinase (MtSK) assay. Aggregation of hit compounds was characterized using multiple experimental methods, LC-MS, 1HNMR, dynamic light scattering (DLS), transmission electron microscopy (TEM), and visual inspection after centrifugation for orthogonal confirmation. Our results suggest that the investigated compounds containing oxadiazole-amide and aminobenzothiazole moieties are false positive hits and non-specific inhibitors of MtSK through aggregate formation.
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212
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Cross JB. Methods for Virtual Screening of GPCR Targets: Approaches and Challenges. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1705:233-264. [PMID: 29188566 DOI: 10.1007/978-1-4939-7465-8_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Virtual screening (VS) has become an integral part of the drug discovery process and is a valuable tool for finding novel chemical starting points for GPCR targets. Ligand-based VS makes use of biochemical data for known, active compounds and has been applied successfully to many diverse GPCRs. Recent progress in GPCR X-ray crystallography has made it possible to incorporate detailed structural information into the VS process. This chapter outlines the latest VS techniques along with examples that highlight successful applications of these methods. Best practices for increasing the likelihood of VS success, as well as ongoing challenges, are also discussed.
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Affiliation(s)
- Jason B Cross
- University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA.
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213
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Ghattas MA, Bryce RA, Al Rawashdah S, Atatreh N, Zalloum WA. Comparative Molecular Dynamics Simulation of Aggregating and Non-Aggregating Inhibitor Solutions: Understanding the Molecular Basis of Promiscuity. ChemMedChem 2017; 13:500-506. [PMID: 29058775 DOI: 10.1002/cmdc.201700654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Indexed: 11/08/2022]
Abstract
The presence of false positives in enzyme inhibition assays is a common problem in early drug discovery, especially for compounds that form colloid aggregates in solution. The molecular basis of these aggregates could not be thoroughly explored because of their transient stability. In this study we conducted comparative molecular dynamics (MD) simulations of miconazole, a strong aggregator, and fluconazole, a known non-aggregator. Interestingly, miconazole displays full aggregation within only 50 ns, whilst fluconazole shows no aggregation over the 500 ns simulation. The simulations indicate that the center of the aggregate is densely packed by the hydrophobic groups of miconazole, whereas polar and nonpolar groups comprise the surface to form a micelle-like colloid. The amphiphilic moment and planar nature of the miconazole structure appear to promote its aggregating behavior. The simulations also predict rapid aggregate formation for a second known promiscuous inhibitor, nicardipine. Thus, MD appears to be a useful tool to characterize aggregate-prone inhibitors at molecular-level detail and has the potential to provide useful information for drug discovery and formulation design.
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Affiliation(s)
- Mohammad A Ghattas
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, 64141, UAE
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, M13 9PL, UK
| | - Sara Al Rawashdah
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, 64141, UAE
| | - Noor Atatreh
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain, 64141, UAE
| | - Waleed A Zalloum
- Faculty of Health Sciences, American University of Madaba, Amman, Jordan
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214
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Assay interference and off-target liabilities of reported histone acetyltransferase inhibitors. Nat Commun 2017; 8:1527. [PMID: 29142305 PMCID: PMC5688144 DOI: 10.1038/s41467-017-01657-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 10/06/2017] [Indexed: 12/20/2022] Open
Abstract
Many compounds with potentially reactive chemical motifs and poor physicochemical properties are published as selective modulators of biomolecules without sufficient validation and then propagated in the scientific literature as useful chemical probes. Several histone acetyltransferase (HAT) inhibitors with these liabilities are now routinely used to probe epigenetic pathways. We profile the most commonly used HAT inhibitors and confirm that the majority of them are nonselective interference compounds. Most (15 out of 23, 65%) of the inhibitors are flagged by ALARM NMR, an industry-developed counter-screen for promiscuous compounds. Biochemical counter-screens confirm that most of these compounds are either thiol-reactive or aggregators. Selectivity panels show many of these compounds modulate unrelated targets in vitro, while several also demonstrate nonspecific effects in cell assays. These data demonstrate the usefulness of performing counter-screens for bioassay promiscuity and assay interference, and raise caution about the utility of many widely used, but insufficiently validated, compounds employed in chemical biology. A substantial obstacle in basic research is the use of poorly validated tool compounds with purported useful biological functions. Here, the authors systematically profile widely used histone acetyltransferase inhibitors and find that the majority are nonselective interference compounds.
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215
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Cannalire R, Tarantino D, Astolfi A, Barreca ML, Sabatini S, Massari S, Tabarrini O, Milani M, Querat G, Mastrangelo E, Manfroni G, Cecchetti V. Functionalized 2,1-benzothiazine 2,2-dioxides as new inhibitors of Dengue NS5 RNA-dependent RNA polymerase. Eur J Med Chem 2017; 143:1667-1676. [PMID: 29137867 DOI: 10.1016/j.ejmech.2017.10.064] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/05/2017] [Accepted: 10/23/2017] [Indexed: 12/11/2022]
Abstract
Over recent years, many RNA viruses have been "re-discovered", including life-threatening flaviviruses, such as Dengue, Zika, and several encephalitis viruses. Since no specific inhibitors are currently available to treat these infections, there is a pressing need for new therapeutics. Among the flaviviral proteins, NS5 RNA-dependent RNA polymerase (RdRp) represents a validated target being essential for viral replication and it has no human analog. To date, few NS5 RdRp inhibitor chemotypes have been reported and no inhibitors are currently in clinical development. In this context, after an in vitro screening against Dengue 3 NS5 RdRp of our in-house HCV NS5B inhibitors focused library, we found that 2,1-benzothiazine 2,2-dioxides are promising non-nucleoside inhibitors of flaviviral RdRp with compounds 8 and 10 showing IC50 of 0.6 and 0.9 μM, respectively. Preliminary structure-activity relationships indicated a key role for the C-4 benzoyl group and the importance of a properly functionalized C-6 phenoxy moiety to modulate potency. Compound 8 acts as non-competitive inhibitor and its proposed pose in the so-called N pocket of the RdRp thumb domain allowed to explain the key contribution of the benzoyl and the phenoxy moieties for the ligand binding.
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Affiliation(s)
- Rolando Cannalire
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via del Liceo, 1-06123 Perugia, Italy
| | - Delia Tarantino
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy; CNR-IBF, Consiglio Nazionale delle Ricerche, Istituto di Biofisica, Via Celoria 26, I-20133 Milano, Italy
| | - Andrea Astolfi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via del Liceo, 1-06123 Perugia, Italy
| | - Maria Letizia Barreca
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via del Liceo, 1-06123 Perugia, Italy
| | - Stefano Sabatini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via del Liceo, 1-06123 Perugia, Italy
| | - Serena Massari
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via del Liceo, 1-06123 Perugia, Italy
| | - Oriana Tabarrini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via del Liceo, 1-06123 Perugia, Italy
| | - Mario Milani
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy; CNR-IBF, Consiglio Nazionale delle Ricerche, Istituto di Biofisica, Via Celoria 26, I-20133 Milano, Italy
| | - Gilles Querat
- UMR "Emergence des Pathologies Virales" (Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP) & Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Faculté de Médecine, 27 bd Jean Moulin, 13005 Marseille France
| | - Eloise Mastrangelo
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, I-20133 Milano, Italy; CNR-IBF, Consiglio Nazionale delle Ricerche, Istituto di Biofisica, Via Celoria 26, I-20133 Milano, Italy.
| | - Giuseppe Manfroni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via del Liceo, 1-06123 Perugia, Italy.
| | - Violetta Cecchetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via del Liceo, 1-06123 Perugia, Italy
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216
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Chen J, Song Y, Bojadzic D, Tamayo-Garcia A, Landin AM, Blomberg BB, Buchwald P. Small-Molecule Inhibitors of the CD40-CD40L Costimulatory Protein-Protein Interaction. J Med Chem 2017; 60:8906-8922. [PMID: 29024591 PMCID: PMC5823691 DOI: 10.1021/acs.jmedchem.7b01154] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Costimulatory interactions are required for T cell activation and development of an effective immune response; hence, they are valuable therapeutic targets for immunomodulation. However, they, as all other protein-protein interactions, are difficult to target by small molecules. Here, we report the identification of novel small-molecule inhibitors of the CD40-CD40L interaction designed starting from the chemical space of organic dyes. For the most promising compounds such as DRI-C21045, activity (IC50) in the low micromolar range has been confirmed in cell assays including inhibition of CD40L-induced activation in NF-κB sensor cells, THP-1 myeloid cells, and primary human B cells as well as in murine allogeneic skin transplant and alloantigen-induced T cell expansion in draining lymph node experiments. Specificity versus other TNF-superfamily interactions (TNF-R1-TNF-α) and lack of cytotoxicity have also been confirmed at these concentrations. These novel compounds provide proof-of-principle evidence for the possibility of small-molecule inhibition of costimulatory protein-protein interactions, establish the structural requirements needed for efficient CD40-CD40L inhibition, and serve to guide the search for such immune therapeutics.
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Affiliation(s)
- Jinshui Chen
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Yun Song
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
- Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Damir Bojadzic
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Alejandro Tamayo-Garcia
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Ana Marie Landin
- Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Bonnie B. Blomberg
- Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Peter Buchwald
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
- Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
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217
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Witten MR, Wissler L, Snow M, Geschwindner S, Read JA, Brandon NJ, Nairn AC, Lombroso PJ, Käck H, Ellman JA. X-ray Characterization and Structure-Based Optimization of Striatal-Enriched Protein Tyrosine Phosphatase Inhibitors. J Med Chem 2017; 60:9299-9319. [PMID: 29116812 DOI: 10.1021/acs.jmedchem.7b01292] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Excessive activity of striatal-enriched protein tyrosine phosphatase (STEP) in the brain has been detected in numerous neuropsychiatric disorders including Alzheimer's disease. Notably, knockdown of STEP in an Alzheimer mouse model effected an increase in the phosphorylation levels of downstream STEP substrates and a significant reversal in the observed cognitive and memory deficits. These data point to the promising potential of STEP as a target for drug discovery in Alzheimer's treatment. We previously reported a substrate-based approach to the development of low molecular weight STEP inhibitors with Ki values as low as 7.8 μM. Herein, we disclose the first X-ray crystal structures of inhibitors bound to STEP and the surprising finding that they occupy noncoincident binding sites. Moreover, we utilize this structural information to optimize the inhibitor structure to achieve a Ki of 110 nM, with 15-60-fold selectivity across a series of phosphatases.
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Affiliation(s)
- Michael R Witten
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Lisa Wissler
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Gothenburg, Sweden
| | - Melanie Snow
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Macclesfield SK10 4TG, United Kingdom
| | - Stefan Geschwindner
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Gothenburg, Sweden
| | - Jon A Read
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Cambridge CB4 0WG, United Kingdom
| | - Nicholas J Brandon
- Neuroscience, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Cambridge, Massachusetts 02139, United States
| | - Angus C Nairn
- Department of Psychiatry, Yale University , New Haven, Connecticut 06520, United States
| | - Paul J Lombroso
- Department of Psychiatry, Yale University , New Haven, Connecticut 06520, United States.,Child Study Center, Yale University , New Haven, Connecticut 06520, United States
| | - Helena Käck
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Gothenburg, Sweden
| | - Jonathan A Ellman
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
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218
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Kenny PW. Comment on The Ecstasy and Agony of Assay Interference Compounds. J Chem Inf Model 2017; 57:2640-2645. [DOI: 10.1021/acs.jcim.7b00313] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Peter W. Kenny
- Berwick-on-Sea, North Coast Road, Blanchisseuse, Saint George, Trinidad and Tobago
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219
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Jasial S, Bajorath J. Dark chemical matter in public screening assays and derivation of target hypotheses. MEDCHEMCOMM 2017; 8:2100-2104. [PMID: 30108727 DOI: 10.1039/c7md00426e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/20/2017] [Indexed: 11/21/2022]
Abstract
Compounds that are consistently inactive in many screening assays, so-called dark chemical matter (DCM), have recently experienced increasing attention. One of the reasons is that many DCM compounds may not be fully inert biologically, but may provide interesting leads for obtaining compounds that are highly selective or active against unusual targets. In this study, we have systematically identified DCM among extensively assayed screening compounds and searched for analogs of these compounds that have known bioactivities. Analog series containing DCM and known bioactive compounds were generated on a large scale, making it possible to derive target hypotheses for more than 8000 extensively assayed DCM molecules.
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Affiliation(s)
- Swarit Jasial
- Department of Life Science Informatics , B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry , Rheinische Friedrich-Wilhelms-Universität , Dahlmannstr. 2 , D-53113 Bonn , Germany . ; ; Tel: +49 228 2699 306
| | - Jürgen Bajorath
- Department of Life Science Informatics , B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry , Rheinische Friedrich-Wilhelms-Universität , Dahlmannstr. 2 , D-53113 Bonn , Germany . ; ; Tel: +49 228 2699 306
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220
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Vo CD, Shebert HL, Zikovich S, Dryer RA, Huang TP, Moran LJ, Cho J, Wassarman DR, Falahee BE, Young PD, Gu GH, Heinl JF, Hammond JW, Jackvony TN, Frederick TE, Blair JA. Repurposing Hsp90 inhibitors as antibiotics targeting histidine kinases. Bioorg Med Chem Lett 2017; 27:5235-5244. [PMID: 29110989 DOI: 10.1016/j.bmcl.2017.10.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/05/2017] [Accepted: 10/18/2017] [Indexed: 01/15/2023]
Abstract
To address the growing need for new antimicrobial agents, we explored whether inhibition of bacterial signaling machinery could inhibit bacterial growth. Because bacteria rely on two-component signaling systems to respond to environmental changes, and because these systems are both highly conserved and mediated by histidine kinases, inhibiting histidine kinases may provide broad spectrum antimicrobial activity. The histidine kinase ATP binding domain is conserved with the ATPase domain of eukaryotic Hsp90 molecular chaperones. To find a chemical scaffold for compounds that target histidine kinases, we leveraged this conservation. We screened ATP competitive Hsp90 inhibitors against CckA, an essential histidine kinase in Caulobacter crescentus that controls cell growth, and showed that the diaryl pyrazole is a promising scaffold for histidine kinase inhibition. We synthesized a panel of derivatives and found that they inhibit the histidine kinases C. crescentus CckA and Salmonella PhoQ but not C. crescentus DivJ; and they inhibit bacterial growth in both Gram-negative and Gram-positive bacterial strains.
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Affiliation(s)
- Chau D Vo
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - Hanna L Shebert
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - Shannon Zikovich
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - Rebecca A Dryer
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - Tony P Huang
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - Lindsey J Moran
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - Juno Cho
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - Douglas R Wassarman
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - Bryn E Falahee
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - Peter D Young
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - Garrick H Gu
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - James F Heinl
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - John W Hammond
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - Taylor N Jackvony
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA
| | - Thomas E Frederick
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jimmy A Blair
- Williams College, Department of Chemistry, 47 Lab Campus Drive, Williamstown, MA 01267, USA.
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221
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Biogenetic Relationships of Bioactive Sponge Merotriterpenoids. Mar Drugs 2017; 15:md15090285. [PMID: 28891968 PMCID: PMC5618424 DOI: 10.3390/md15090285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/07/2017] [Accepted: 09/07/2017] [Indexed: 02/01/2023] Open
Abstract
Hydroquinone meroterpenoids, especially those derived from marine sponges, display a wide range of biological activities. However, use of these compounds is limited by their inaccessibility; there is no sustainable supply of these compounds. Furthermore, our knowledge of their metabolic origin remains completely unstudied. In this review, an in depth structural analysis of sponge merotriterpenoids, including the adociasulfate family of kinesin motor protein inhibitors, provides insight into their biosynthesis. Several key structural features provide clues to the relationships between compounds. All adociasulfates appear to be derived from only four different hydroquinone hexaprenyl diphosphate precursors, each varying in the number and position of epoxidations. Proton-initiated cyclization of these precursors can lead to all carbon skeletons observed amongst sponge merotriterpenoids. Consideration of the enzymes involved in the proposed biosynthetic route suggests a bacterial source, and a hypothetical gene cluster was constructed that may facilitate discovery of the authentic pathway from the sponge metagenome. A similar rationale can be extended to other sponge meroterpenoids, for which no biosynthetic pathways have yet been identified.
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222
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Stark T, Lieblein T, Pohland M, Kalden E, Freund P, Zangl R, Grewal R, Heilemann M, Eckert GP, Morgner N, Göbel MW. Peptidomimetics That Inhibit and Partially Reverse the Aggregation of Aβ1–42. Biochemistry 2017; 56:4840-4849. [DOI: 10.1021/acs.biochem.7b00223] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | | | | | | | | | - Rekha Grewal
- Institute
of Nutritional Sciences, Justus-Liebig-University Giessen, Wilhelmstrasse
20, D-35392 Giessen, Germany
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223
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Synthetic Cyclic Peptomers as Type III Secretion System Inhibitors. Antimicrob Agents Chemother 2017; 61:AAC.00060-17. [PMID: 28652236 DOI: 10.1128/aac.00060-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 06/10/2017] [Indexed: 12/12/2022] Open
Abstract
Antibiotic-resistant bacteria are an emerging threat to global public health. New classes of antibiotics and tools for antimicrobial discovery are urgently needed. Type III secretion systems (T3SS), which are required by dozens of Gram-negative bacteria for virulence but largely absent from nonpathogenic bacteria, are promising virulence blocker targets. The ability of mammalian cells to recognize the presence of a functional T3SS and trigger NF-κB activation provides a rapid and sensitive method for identifying chemical inhibitors of T3SS activity. In this study, we generated a HEK293 stable cell line expressing green fluorescent protein (GFP) driven by a promoter containing NF-κB enhancer elements to serve as a readout of T3SS function. We identified a family of synthetic cyclic peptide-peptoid hybrid molecules (peptomers) that exhibited dose-dependent inhibition of T3SS effector secretion in Yersinia pseudotuberculosis and Pseudomonas aeruginosa without affecting bacterial growth or motility. Among these inhibitors, EpD-3'N, EpD-1,2N, EpD-1,3'N, EpD-1,2,3'N, and EpD-1,2,4'N exhibited strong inhibitory effects on translocation of the Yersinia YopM effector protein into mammalian cells (>40% translocation inhibition at 7.5 μM) and showed no toxicity to mammalian cells at 240 μM. In addition, EpD-3'N and EpD-1,2,4'N reduced the rounding of HeLa cells caused by the activity of Yersinia effector proteins that target the actin cytoskeleton. In summary, we have discovered a family of novel cyclic peptomers that inhibit the injectisome T3SS but not the flagellar T3SS.
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224
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Ehlert FGR, Linde K, Diederich WE. What Are We Missing? The Detergent Triton X-100 Added to Avoid Compound Aggregation Can Affect Assay Results in an Unpredictable Manner. ChemMedChem 2017; 12:1419-1423. [PMID: 28745428 DOI: 10.1002/cmdc.201700329] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/19/2017] [Indexed: 11/07/2022]
Abstract
In this study we show that the detergent Triton X-100, which is widely used in screening campaigns, significantly decreases the binding affinities of some known specific inhibitors of HIV-1 protease and the well-established model protease endothiapepsin in a fluorescence-based assay. Surprisingly, other structurally related inhibitors remain entirely unaffected. As a consequence, those compounds that were affected would most likely have been misclassified as unspecific binders, although they are actually true positives, and thus could be considered excellent starting points for further hit optimization.
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Affiliation(s)
- Fabian G R Ehlert
- Zentrum für Tumor- und Immunbiologie und Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 3, 35043, Marburg, Germany
| | - Kerstin Linde
- Zentrum für Tumor- und Immunbiologie und Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 3, 35043, Marburg, Germany
| | - Wibke E Diederich
- Zentrum für Tumor- und Immunbiologie und Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 3, 35043, Marburg, Germany
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225
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Gilberg E, Stumpfe D, Bajorath J. Towards a systematic assessment of assay interference: Identification of extensively tested compounds with high assay promiscuity. F1000Res 2017; 6. [PMID: 28928939 PMCID: PMC5596351 DOI: 10.12688/f1000research.12370.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/11/2017] [Indexed: 12/16/2022] Open
Abstract
A large-scale statistical analysis of hit rates of extensively assayed compounds is presented to provide a basis for a further assessment of assay interference potential and multi-target activities. A special feature of this investigation has been the inclusion of compound series information in activity analysis and the characterization of analog series using different parameters derived from assay statistics. No prior knowledge of compounds or targets was taken into consideration in the data-driven study of analog series. It was anticipated that taking large volumes of activity data, assay frequency, and assay overlap information into account would lead to statistically sound and chemically meaningful results. More than 6000 unique series of analogs with high hit rates were identified, more than 5000 of which did not contain known interference candidates, hence providing ample opportunities for follow-up analyses from a medicinal chemistry perspective.
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Affiliation(s)
- Erik Gilberg
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53113, Germany
| | - Dagmar Stumpfe
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53113, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53113, Germany
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226
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Gilberg E, Stumpfe D, Bajorath J. Towards a systematic assessment of assay interference: Identification of extensively tested compounds with high assay promiscuity. F1000Res 2017; 6. [PMID: 28928939 DOI: 10.12688/f1000research.12370.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/16/2017] [Indexed: 11/20/2022] Open
Abstract
A large-scale statistical analysis of hit rates of extensively assayed compounds is presented to provide a basis for a further assessment of assay interference potential and multi-target activities. A special feature of this investigation has been the inclusion of compound series information in activity analysis and the characterization of analog series using different parameters derived from assay statistics. No prior knowledge of compounds or targets was taken into consideration in the data-driven study of analog series. It was anticipated that taking large volumes of activity data, assay frequency, and assay overlap information into account would lead to statistically sound and chemically meaningful results. More than 6000 unique series of analogs with high hit rates were identified, more than 5000 of which did not contain known interference candidates, hence providing ample opportunities for follow-up analyses from a medicinal chemistry perspective.
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Affiliation(s)
- Erik Gilberg
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53113, Germany
| | - Dagmar Stumpfe
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53113, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, D-53113, Germany
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227
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Dalvit C, Santi S, Neier R. A Ligand‐Based NMR Screening Approach for the Identification and Characterization of Inhibitors and Promoters of Amyloid Peptide Aggregation. ChemMedChem 2017; 12:1458-1463. [DOI: 10.1002/cmdc.201700319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/20/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Claudio Dalvit
- Department of ChemistryUniversity of Neuchatel Avenue de Bellevaux 51 2000 Neuchatel Switzerland
| | - Sara Santi
- Department of ChemistryUniversity of Neuchatel Avenue de Bellevaux 51 2000 Neuchatel Switzerland
| | - Reinhard Neier
- Department of ChemistryUniversity of Neuchatel Avenue de Bellevaux 51 2000 Neuchatel Switzerland
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228
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Lorenz DA, Vander Roest S, Larsen MJ, Garner AL. Development and Implementation of an HTS-Compatible Assay for the Discovery of Selective Small-Molecule Ligands for Pre-microRNAs. SLAS DISCOVERY 2017; 23:47-54. [PMID: 28686847 DOI: 10.1177/2472555217717944] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
microRNAs (miRNAs) are small gene regulatory RNAs, and their expression has been found to be dysregulated in a number of human diseases. To facilitate the discovery of small molecules capable of selectively modulating the activity of a specific miRNA, we have utilized new high-throughput screening technology targeting Dicer-mediated pre-miRNA maturation. Pilot screening of ~50,000 small molecules and ~33,000 natural product extract libraries against pre-miR-21 processing indicated the potential of our assay for this goal, yielding a campaign Z' factor of 0.52 and an average plate signal-to-background (S/B) ratio of 13. Using two-dimensional screening against a second pre-miRNA, pre-let-7d, we evaluated the selectivity of confirmed hits. The results presented demonstrate how high-throughput screening can be used to identify selective small molecules for a target RNA.
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Affiliation(s)
- Daniel A Lorenz
- 1 Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Steve Vander Roest
- 3 Center for Chemical Genomics, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Martha J Larsen
- 3 Center for Chemical Genomics, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Amanda L Garner
- 1 Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA.,2 Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
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229
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Identification of Antifungal H +-ATPase Inhibitors with Effect on Plasma Membrane Potential. Antimicrob Agents Chemother 2017; 61:AAC.00032-17. [PMID: 28438931 PMCID: PMC5487681 DOI: 10.1128/aac.00032-17] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/15/2017] [Indexed: 02/07/2023] Open
Abstract
The plasma membrane H+-ATPase (Pma1) is an essential fungal protein and a proposed target for new antifungal medications. The compounds in a small-molecule library containing ∼191,000 commercially available compounds were screened for their ability to inhibit Saccharomyces cerevisiae plasma membranes containing Pma1. The overall hit rate was 0.2%, corresponding to 407 compounds. These hit compounds were further evaluated for ATPase selectivity and broad-spectrum antifungal activity. Following this work, one Pma1 inhibitor series based on compound 14 and analogs was selected for further evaluation. This compound series was able to depolarize the membrane and inhibit extracellular acidification in intact fungal cells concomitantly with a significant increase in intracellular ATP levels. Collectively, we suggest that these effects may be a common feature of Pma1 inhibitors. Additionally, the work uncovered a dual mechanism for the previously identified cationic peptide BM2, revealing fungal membrane disruption, in addition to Pma1 inhibition. The methods presented here provide a solid platform for the evaluation of Pma1-specific inhibitors in a drug development setting. The present inhibitors could serve as a starting point for the development of new antifungal agents with a novel mode of action.
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230
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Rawson S, McPhillie MJ, Johnson RM, Fishwick CWG, Muench SP. The potential use of single-particle electron microscopy as a tool for structure-based inhibitor design. Acta Crystallogr D Struct Biol 2017; 73:534-540. [PMID: 28580915 PMCID: PMC5458495 DOI: 10.1107/s2059798317004077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/13/2017] [Indexed: 12/14/2022] Open
Abstract
Recent developments in electron microscopy (EM) have led to a step change in our ability to solve the structures of previously intractable systems, especially membrane proteins and large protein complexes. This has provided new opportunities in the field of structure-based drug design, with a number of high-profile publications resolving the binding sites of small molecules and peptide inhibitors. There are a number of advantages of EM over the more traditional X-ray crystallographic approach, such as resolving different conformational states and permitting the dynamics of a system to be better resolved when not constrained by a crystal lattice. There are still significant challenges to be overcome using an EM approach, not least the speed of structure determination, difficulties with low-occupancy ligands and the modest resolution that is available. However, with the anticipated developments in the field of EM, the potential of EM to become a key tool for structure-based drug design, often complementing X-ray and NMR studies, seems promising.
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Affiliation(s)
- S. Rawson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - M. J. McPhillie
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - R. M. Johnson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - C. W. G. Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
| | - S. P. Muench
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, England
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231
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Lucas AT, Herity LB, Kornblum ZA, Madden AJ, Gabizon A, Kabanov AV, Ajamie RT, Bender DM, Kulanthaivel P, Sanchez-Felix MV, Havel HA, Zamboni WC. Pharmacokinetic and screening studies of the interaction between mononuclear phagocyte system and nanoparticle formulations and colloid forming drugs. Int J Pharm 2017; 526:443-454. [DOI: 10.1016/j.ijpharm.2017.04.079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 04/27/2017] [Accepted: 04/30/2017] [Indexed: 02/08/2023]
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232
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Ganesh AN, Logie J, McLaughlin CK, Barthel BL, Koch TH, Shoichet BK, Shoichet MS. Leveraging Colloidal Aggregation for Drug-Rich Nanoparticle Formulations. Mol Pharm 2017; 14:1852-1860. [PMID: 28502177 DOI: 10.1021/acs.molpharmaceut.6b01015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While limited drug loading continues to be problematic for chemotherapeutics formulated in nanoparticles, we found that we could take advantage of colloidal drug aggregation to achieve high loading when combined with polymeric excipients. We demonstrate this approach with two drugs, fulvestrant and pentyl-PABC doxazolidine (PPD; a prodrug of doxazolidine, which is a DNA cross-linking anthracycline), and two polymers, polysorbate 80 (UP80) and poly(d,l-lactide-co-2-methyl-2-carboxytrimethylene carbonate)-graft-poly(ethylene glycol) (PLAC-PEG; a custom-synthesized, self-assembling amphiphilic polymer). In both systems, drug-loaded nanoparticles had diameters < 200 nm and were stable for up to two days in buffered saline solution and for up to 24 h in serum-containing media at 37 °C. While colloidal drug aggregates alone are typically unstable in saline and serum-containing media, we attribute the colloid stability observed herein to the polymeric excipients and consequent decreased protein adsorption. We expect this strategy of polymer-stabilized colloidal drug aggregates to be broadly applicable in delivery formulations.
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Affiliation(s)
- Ahil N Ganesh
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada M5S 3E5.,Institute of Biomaterials and Biomedical Engineering, University of Toronto , 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Jennifer Logie
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada M5S 3E5.,Institute of Biomaterials and Biomedical Engineering, University of Toronto , 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Christopher K McLaughlin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada M5S 3E5.,Institute of Biomaterials and Biomedical Engineering, University of Toronto , 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Benjamin L Barthel
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Tad H Koch
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry & Quantitative Biology Institute, University of California, San Francisco , 1700 Fourth Street, Mail Box 2550, San Francisco, California 94143, United States
| | - Molly S Shoichet
- Department of Chemical Engineering and Applied Chemistry, University of Toronto , 200 College Street, Toronto, Ontario, Canada M5S 3E5.,Institute of Biomaterials and Biomedical Engineering, University of Toronto , 164 College Street, Toronto, Ontario, Canada M5S 3G9.,Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario, Canada M5S 3H6
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233
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS Infect Dis 2017; 3:259-262. [PMID: 28244723 DOI: 10.1021/acsinfecdis.7b00023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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234
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS Med Chem Lett 2017; 8:379-382. [PMID: 28435522 DOI: 10.1021/acsmedchemlett.7b00056] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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235
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Ganesh AN, McLaughlin CK, Duan D, Shoichet BK, Shoichet MS. A New Spin on Antibody-Drug Conjugates: Trastuzumab-Fulvestrant Colloidal Drug Aggregates Target HER2-Positive Cells. ACS APPLIED MATERIALS & INTERFACES 2017; 9:12195-12202. [PMID: 28319364 PMCID: PMC5486225 DOI: 10.1021/acsami.6b15987] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
While the formation of colloidal aggregates leads to artifacts in early drug discovery, their composition makes them attractive as nanoparticle formulations for targeted drug delivery as the entire nanoparticle is composed of drug. The typical transient stability of colloidal aggregates has inhibited exploiting this property. To overcome this limitation, we investigated a series of proteins to stabilize colloidal aggregates of the chemotherapeutic, fulvestrant, including the following: bovine serum albumin, a generic human immunoglobulin G, and trastuzumab, a therapeutic human epidermal growth factor receptor 2 antibody. Protein coronas reduced colloid size to <300 nm and improved their stability to over 48 h in both buffered saline and media containing serum protein. Unlike colloids stabilized with other proteins, trastuzumab-fulvestrant colloids were taken up by HER2 overexpressing cells and were cytotoxic. This new targeted formulation reimagines antibody-drug conjugates, delivering mM concentrations of drug to a cell.
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Affiliation(s)
- Ahil N. Ganesh
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Christopher K. McLaughlin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - Da Duan
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
- Department of Pharmaceutical Chemistry & Quantitative Biology Institute, University of California, San Francisco, 1700 Fourth Street, Mail Box 2550, San Francisco, California 94143, United States
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry & Quantitative Biology Institute, University of California, San Francisco, 1700 Fourth Street, Mail Box 2550, San Francisco, California 94143, United States
- Corresponding Authors: (M.S.S.) ., (B.K.S.)
| | - Molly S. Shoichet
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, Canada M5S 3E5
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada M5S 3H6
- Corresponding Authors: (M.S.S.) ., (B.K.S.)
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236
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Zhang R, Yu R, Xu Q, Li X, Luo J, Jiang B, Wang L, Guo S, Wu N, Shi D. Discovery and evaluation of the hybrid of bromophenol and saccharide as potent and selective protein tyrosine phosphatase 1B inhibitors. Eur J Med Chem 2017; 134:24-33. [PMID: 28395151 DOI: 10.1016/j.ejmech.2017.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/21/2017] [Accepted: 04/02/2017] [Indexed: 11/28/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a key negative regulator of insulin signaling pathway. Inhibition of PTP1B is expected to improve insulin action. Appropriate selectivity and permeability are the gold standard for excellent PTP1B inhibitors. In this work, molecular hybridization-based screening identified a selective competitive PTP1B inhibitor. Compound 10a has IC50 values of 199 nM against PTP1B, and shows 32-fold selectivity for PTP1B over the closely related phosphatase TCPTP. Molecule docking and molecular dynamics studies reveal the reason of selectivity for PTP1B over TCPTP. Moreover, the cell permeability and cellular activity of compound 10a are demonstrated respectively.
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Affiliation(s)
- Renshuai Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Rilei Yu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Qi Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiangqian Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jiao Luo
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Bo Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lijun Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shuju Guo
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ning Wu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Dayong Shi
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
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237
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Abstract
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Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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238
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS CENTRAL SCIENCE 2017; 3:143-147. [PMID: 28386587 PMCID: PMC5364449 DOI: 10.1021/acscentsci.7b00069] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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239
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS Chem Biol 2017; 12:575-578. [PMID: 28244728 DOI: 10.1021/acschembio.7b00119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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240
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Blevitt JM, Hack MD, Herman KL, Jackson PF, Krawczuk PJ, Lebsack AD, Liu AX, Mirzadegan T, Nelen MI, Patrick AN, Steinbacher S, Milla ME, Lumb KJ. Structural Basis of Small-Molecule Aggregate Induced Inhibition of a Protein-Protein Interaction. J Med Chem 2017; 60:3511-3517. [PMID: 28300404 DOI: 10.1021/acs.jmedchem.6b01836] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A prevalent observation in high-throughput screening and drug discovery programs is the inhibition of protein function by small-molecule compound aggregation. Here, we present the X-ray structural description of aggregation-based inhibition of a protein-protein interaction involving tumor necrosis factor α (TNFα). An ordered conglomerate of an aggregating small-molecule inhibitor (JNJ525) induces a quaternary structure switch of TNFα that inhibits the protein-protein interaction between TNFα and TNFα receptors. SPD-304 may employ a similar mechanism of inhibition.
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Affiliation(s)
- Jonathan M Blevitt
- Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , La Jolla, California 92121, United States
| | - Michael D Hack
- Lead Discovery, Discovery Sciences, Janssen R&D LLC , La Jolla, California 92121, United States
| | - Krystal L Herman
- Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , La Jolla, California 92121, United States
| | - Paul F Jackson
- Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , La Jolla, California 92121, United States
| | - Paul J Krawczuk
- Immunology, Janssen R&D LLC , Spring House, Pennsylvania 19477, United States
| | - Alec D Lebsack
- Immunology, Janssen R&D LLC , La Jolla, California 92121, United States
| | - Annie X Liu
- Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , Spring House, Pennsylvania 19477, United States
| | - Taraneh Mirzadegan
- Lead Discovery, Discovery Sciences, Janssen R&D LLC , La Jolla, California 92121, United States
| | - Marina I Nelen
- Lead Discovery, Discovery Sciences, Janssen R&D LLC , Spring House, Pennsylvania 19477, United States
| | - Aaron N Patrick
- Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , Spring House, Pennsylvania 19477, United States
| | | | - Marcos E Milla
- Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , La Jolla, California 92121, United States
| | - Kevin J Lumb
- Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , Spring House, Pennsylvania 19477, United States
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241
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS Chem Neurosci 2017; 8:420-423. [PMID: 28244737 DOI: 10.1021/acschemneuro.7b00064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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242
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Hu Y, Jasial S, Gilberg E, Bajorath J. Structure-Promiscuity Relationship Puzzles-Extensively Assayed Analogs with Large Differences in Target Annotations. AAPS JOURNAL 2017; 19:856-864. [PMID: 28265982 DOI: 10.1208/s12248-017-0066-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/21/2017] [Indexed: 01/18/2023]
Abstract
Publicly available screening data were systematically searched for extensively assayed structural analogs with large differences in the number of targets they were active against. Screening compounds with potential chemical liabilities that may give rise to assay artifacts were identified and excluded from the analysis. "Promiscuity cliffs" were frequently identified, defined here as pairs of structural analogs with a difference of at least 20 target annotations across all assays they were tested in. New assay indices were introduced to prioritize cliffs formed by screening compounds that were extensively tested in comparably large numbers of assays including many shared assays. In these cases, large differences in promiscuity degrees were not attributable to differences in assay frequency and/or lack of assay overlap. Such analog pairs have high priority for further exploring molecular origins of multi-target activities. Therefore, these promiscuity cliffs and associated target annotations are made freely available. The corresponding analogs often represent equally puzzling and interesting examples of structure-promiscuity relationships.
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Affiliation(s)
- Ye Hu
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Dahlmannstr. 2, 53113, Bonn, Germany
| | - Swarit Jasial
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Dahlmannstr. 2, 53113, Bonn, Germany
| | - Erik Gilberg
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Dahlmannstr. 2, 53113, Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Dahlmannstr. 2, 53113, Bonn, Germany.
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243
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Entering the 'big data' era in medicinal chemistry: molecular promiscuity analysis revisited. Future Sci OA 2017; 3:FSO179. [PMID: 28670471 PMCID: PMC5481856 DOI: 10.4155/fsoa-2017-0001] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 01/26/2017] [Indexed: 12/26/2022] Open
Abstract
The 'big data' concept plays an increasingly important role in many scientific fields. Big data involves more than unprecedentedly large volumes of data that become available. Different criteria characterizing big data must be carefully considered in computational data mining, as we discuss herein focusing on medicinal chemistry. This is a scientific discipline where big data is beginning to emerge and provide new opportunities. For example, the ability of many drugs to specifically interact with multiple targets, termed promiscuity, forms the molecular basis of polypharmacology, a hot topic in drug discovery. Compound promiscuity analysis is an area that is much influenced by big data phenomena. Different results are obtained depending on chosen data selection and confidence criteria, as we also demonstrate.
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244
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245
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. J Chem Inf Model 2017; 57:387-390. [PMID: 28244743 DOI: 10.1021/acs.jcim.7b00105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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246
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. Biochemistry 2017; 56:1363-1366. [PMID: 28244742 DOI: 10.1021/acs.biochem.7b00110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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247
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. J Med Chem 2017; 60:2165-2168. [PMID: 28244745 DOI: 10.1021/acs.jmedchem.7b00229] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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248
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Abstract
Designing drugs that can simultaneously interact with multiple targets is a promising approach for treating complicated diseases. Compared to using combinations of single target drugs, multitarget drugs have advantages of higher efficacy, improved safety profile, and simpler administration. Many in silico methods have been developed to approach different aspects of this polypharmacology-guided drug design, particularly for drug repurposing and multitarget drug design. In this review, we summarize recent progress in computational multitarget drug design and discuss their advantages and limitations. Perspectives for future drug development will also be discussed.
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Affiliation(s)
- Weilin Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies (AAIS), Peking University , Beijing 100871, People's Republic of China
| | - Jianfeng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies (AAIS), Peking University , Beijing 100871, People's Republic of China
| | - Luhua Lai
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies (AAIS), Peking University , Beijing 100871, People's Republic of China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies (AAIS), Peking University , Beijing 100871, People's Republic of China.,BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, People's Republic of China
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249
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Waqas M, Jeong WJ, Lee YJ, Kim DH, Ryou C, Lim YB. pH-Dependent In-Cell Self-Assembly of Peptide Inhibitors Increases the Anti-Prion Activity While Decreasing the Cytotoxicity. Biomacromolecules 2017; 18:943-950. [PMID: 28128930 DOI: 10.1021/acs.biomac.6b01816] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The first step in the conventional approach to self-assembled biomaterials is to develop well-defined nanostructures in vitro, which is followed by disruption of the preformed nanostructures at the inside of the cell to achieve bioactivity. Here, we propose an inverse strategy to develop in-cell gain-of-function self-assembled nanostructures. In this approach, the supramolecular building blocks exist in a unimolecular/unordered state in vitro or at the outside of the cell and assemble into well-defined nanostructures after cell internalization. We used block copolypeptides of an oligoarginine and a self-assembling peptide as building blocks and investigated correlations among the nanostructural state, antiprion bioactivity, and cytotoxicity. The optimal bioactivity (i.e., the highest antiprion activity and lowest cytotoxicity) was obtained when the building blocks existed in a unimolecular/unordered state in vitro and during the cell internalization process, exerting minimal cytotoxic damage to cell membranes, and were subsequently converted into high-charge-density vesicles in the low pH endosome/lysosomes in vivo, thus, resulting in the significantly enhanced antiprion activity. In particular, the in-cell self-assembly concept presents a feasible approach to developing therapeutics against protein misfolding diseases. In general, the in-cell self-assembly provides a novel inverse methodology to supramolecular bionanomaterials.
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Affiliation(s)
- Muhammad Waqas
- Department of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University , Gyeonggi-do 15588, Republic of Korea
| | - Woo-Jin Jeong
- Department of Materials Science and Engineering, Yonsei University , Seoul 03722, Republic of Korea
| | - Young-Joo Lee
- Department of Materials Science and Engineering, Yonsei University , Seoul 03722, Republic of Korea
| | - Dae-Hwan Kim
- Department of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University , Gyeonggi-do 15588, Republic of Korea
| | - Chongsuk Ryou
- Department of Pharmacy and Institute of Pharmaceutical Science and Technology, Hanyang University , Gyeonggi-do 15588, Republic of Korea
| | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University , Seoul 03722, Republic of Korea
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250
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Cramer J, Schiebel J, Wulsdorf T, Grohe K, Najbauer EE, Ehrmann FR, Radeva N, Zitzer N, Linne U, Linser R, Heine A, Klebe G. Falsch-positiver Treffer im Fragment-basierten Wirkstoffdesign: Lass Dich nicht auf die falsche Fährte locken! Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jonathan Cramer
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Johannes Schiebel
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Tobias Wulsdorf
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Kristof Grohe
- Abteilung für NMR-basierte Strukturbiologie; Max-Planck-Institut für Biophysikalische Chemie; Am Faßberg 11 37077 Göttingen Deutschland
- Fakultät für Chemie und Pharmazie; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13, Haus F 81377 München Deutschland
| | - Eszter Eva Najbauer
- Abteilung für NMR-basierte Strukturbiologie; Max-Planck-Institut für Biophysikalische Chemie; Am Faßberg 11 37077 Göttingen Deutschland
| | - Frederik R. Ehrmann
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Nedyalka Radeva
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Nina Zitzer
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Uwe Linne
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Straße 4 35043 Marburg Deutschland
| | - Rasmus Linser
- Abteilung für NMR-basierte Strukturbiologie; Max-Planck-Institut für Biophysikalische Chemie; Am Faßberg 11 37077 Göttingen Deutschland
- Fakultät für Chemie und Pharmazie; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13, Haus F 81377 München Deutschland
| | - Andreas Heine
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
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