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Structure-based inhibition of protein-protein interactions. Eur J Med Chem 2014; 94:480-8. [PMID: 25253637 DOI: 10.1016/j.ejmech.2014.09.047] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 09/03/2014] [Accepted: 09/12/2014] [Indexed: 12/24/2022]
Abstract
Protein-protein interactions (PPIs) are emerging as attractive targets for drug design because of their central role in directing normal and aberrant cellular functions. These interactions were once considered "undruggable" because their large and dynamic interfaces make small molecule inhibitor design challenging. However, landmark advances in computational analysis, fragment screening and molecular design have enabled development of a host of promising strategies to address the fundamental molecular recognition challenge. An attractive approach for targeting PPIs involves mimicry of protein domains that are critical for complex formation. This approach recognizes that protein subdomains or protein secondary structures are often present at interfaces and serve as organized scaffolds for the presentation of side chain groups that engage the partner protein(s). Design of protein domain mimetics is in principle rather straightforward but is enabled by a host of computational strategies that provide predictions of important residues that should be mimicked. Herein we describe a workflow proceeding from interaction network analysis, to modeling a complex structure, to identifying a high-affinity sub-structure, to developing interaction inhibitors. We apply the design procedure to peptidomimetic inhibitors of Ras-mediated signaling.
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2
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A novel immobilization strategy using oligonucleotide as linker for small molecule microarrays construction. Biosens Bioelectron 2008; 23:1694-700. [PMID: 18346888 DOI: 10.1016/j.bios.2008.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 01/04/2008] [Accepted: 02/06/2008] [Indexed: 11/24/2022]
Abstract
A novel immobilization method based on oligonucleotide as linker has been developed for small molecule microarrays (SMMs) construction. The oligonucleotide tail was employed as a linker in solid-phase synthesis. Small molecules could be easily conjugated at the 5' end of the oligonucleotide, previously modified with a functional group. Being a reactive species, the oligonucleotide was activated by UV irradiation, for the attachment of the conjugate to the slide surface. The method was successfully applied to structurally distinct small molecules, including biotin, antibiotic and drug. This immobilization strategy showed high efficiency, 1.1fmol of small molecules in the spotting solution per spot gave a detectable signal (mean S/N=10.9). The results suggest that it is very promising for exploring interaction between small molecules and proteins, and high throughput detecting the chemical compounds.
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3
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Saxe JP, Wu H, Kelly TK, Phelps ME, Sun YE, Kornblum HI, Huang J. A phenotypic small-molecule screen identifies an orphan ligand-receptor pair that regulates neural stem cell differentiation. ACTA ACUST UNITED AC 2007; 14:1019-30. [PMID: 17884634 PMCID: PMC2758915 DOI: 10.1016/j.chembiol.2007.07.016] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2007] [Revised: 07/18/2007] [Accepted: 07/27/2007] [Indexed: 01/20/2023]
Abstract
High-throughput identification of small molecules that selectively modulate molecular, cellular, or systems-level properties of the mammalian brain is a significant challenge. Here we report the chemical genetic identification of the orphan ligand phosphoserine (P-Ser) as an enhancer of neurogenesis. P-Ser inhibits neural stem cell/progenitor proliferation and self-renewal, enhances neurogenic fate commitment, and improves neuronal survival. We further demonstrate that the effects of P-Ser are mediated by the group III metabotropic glutamate receptor 4 (mGluR4). siRNA-mediated knockdown of mGluR4 abolished the effects of P-Ser and increased neurosphere proliferation, at least in part through upregulation of mTOR pathway activity. We also found that P-Ser increases neurogenesis in human embryonic stem cell-derived neural progenitors. This work highlights the tremendous potential of developing effective small-molecule drugs for use in regenerative medicine or transplantation therapy.
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Affiliation(s)
- Jonathan P. Saxe
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095
| | - Hao Wu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095
| | - Theresa K. Kelly
- The Interdepartmental Graduate Program in the Neurosciences, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095
| | - Michael E. Phelps
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095
| | - Yi E. Sun
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095
- Department of Psychiatry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095
- The Semel Institute for Neuroscience, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095
- To whom correspondence should be addressed: Jing Huang , Harley Kornblum , or Yi Sun
| | - Harley I. Kornblum
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095
- Department of Psychiatry, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095
- Department of Pediatrics, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095
- The Semel Institute for Neuroscience, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095
- To whom correspondence should be addressed: Jing Huang , Harley Kornblum , or Yi Sun
| | - Jing Huang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA 90095
- To whom correspondence should be addressed: Jing Huang , Harley Kornblum , or Yi Sun
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4
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Ahn YH, Chang YT. Tagged small molecule library approach for facilitated chemical genetics. Acc Chem Res 2007; 40:1025-33. [PMID: 17547366 DOI: 10.1021/ar700030k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chemical genetics is a powerful method which utilizes small molecule regulators to reveal the molecular basis of diverse biological processes. However, the current chemical genetic approach sometimes meets a serious bottleneck during the process of target identification. One faces difficulty in conjugating the active compound to an affinity matrix without losing or reducing its activity that leads to laborious structure-activity relationship (SAR) studies. To facilitate this process, we have developed a tagged triazine library containing a built-in linker that provides a straightforward transition from phenotypic screening to target identification. A strategy for constructing a tagged library and applications with a streamlined target identification and subsequent mechanistic study are discussed in this Account.
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Affiliation(s)
- Young-Hoon Ahn
- Department of Chemistry, New York University, New York, New York 10003, USA
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5
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Affiliation(s)
- Daniel P Walsh
- Department of Chemistry, New York University, New York, New York 10003, USA
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6
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Adams DS, Levin M. Inverse drug screens: a rapid and inexpensive method for implicating molecular targets. Genesis 2007; 44:530-40. [PMID: 17078061 PMCID: PMC3142945 DOI: 10.1002/dvg.20246] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Identification of gene products that function in some specific process of interest is a common goal in developmental biology. Although use of drug compounds to probe biological systems has a very long history in teratology and toxicology, systematic hierarchical drug screening has not been capitalized upon by the developmental biology community. This "chemical genetics" approach can greatly benefit the study of embryonic and regenerative systems, and we have formalized a strategy for using known pharmacological compounds to implicate specific molecular candidates in any chosen biological phenomenon. Taking advantage of a hierarchical structure that can be imposed on drug reagents in a number of fields such as ion transport, neurotransmitter function, metabolism, and cytoskeleton, any assay can be carried out as a binary search algorithm. This inverse drug screen methodology is much more efficient than exhaustive testing of large numbers of drugs, and reveals the identity of a manageable number of specific molecular candidates that can then be validated and targeted using more expensive and specific molecular reagents. Here, we describe the process of this loss-of-function screen and illustrate its use in uncovering novel bioelectrical and serotonergic mechanisms in embryonic patterning. This technique is an inexpensive and rapid complement to existing molecular screening strategies. Moreover, it is applicable to maternal proteins, and model species in which traditional genetic screens are not feasible, significantly extending the opportunities to identify key endogenous players in biological processes.
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Affiliation(s)
| | - Michael Levin
- Correspondence to: Michael Levin, Center for Regenerative and Developmental Biology, Forsyth Institute and Developmental Biology Department, Harvard School of Dental Medicine, 140 The Fenway, Boston, MA 02115.
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7
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Tate EW. Chemical intervention in signalling networks: recent advances and applications. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/sita.200500075] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abstract
Diversity-oriented synthesis (DOS) is an emerging field involving the synthesis of combinatorial libraries of diverse small molecules for biological screening. Rather than being directed toward a single biological target, DOS libraries can be used to identify new ligands for a variety of targets. Several different strategies for library design have been developed to target the biologically relevant regions of chemical structure space. DOS has provided powerful probes to investigate biological mechanisms and also served as a new driving force for advancing synthetic organic chemistry.
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Affiliation(s)
- Derek S Tan
- Tri-Institutional Research Program, Memorial Sloan-Kettering Cancer Center, 1275 York Ave., Box 422, New York, New York 10021, USA.
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9
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Gough JD, Crews CM. Probing protein function with small molecules. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2006:61-74. [PMID: 16708999 DOI: 10.1007/978-3-540-37635-4_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The interface of chemistry and biology offers many opportunities to explore different aspects of cell biology. The emerging field of chemical genetics is providing the chemical means to understand biological systems not easily accessible using classical genetic manipulations. In this article, we will discuss how natural product mode of action studies and novel bio-organic manipulation of intracellular protein levels are proving useful in the exploration of cell biology.
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Affiliation(s)
- J D Gough
- Department of Molecular, Cell and Development Biology, New Haven, CT 06520-8103, USA
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Du AY, Zhao BX, Yin DL, Zhang SL, Miao JY. Discovery of a novel small molecule, 1-ethoxy-3-(3,4-methylenedioxyphenyl)-2-propanol, that induces apoptosis in A549 human lung cancer cells. Bioorg Med Chem 2005; 13:4176-83. [PMID: 15886004 DOI: 10.1016/j.bmc.2005.04.031] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Accepted: 04/14/2005] [Indexed: 10/25/2022]
Abstract
A novel small molecule, 1-ethoxy-3-(3,4-methylenedioxyphenyl)-2-propanol (EOD), was synthesized in our laboratory. Previously, we reported pharmacological properties of EOD, triggering apoptosis in Human umbilical vein endothelial cells (HUVECs). Here, we further investigated the effects of EOD on the growth of A549 human lung cancer cells. EOD treatment induced apoptosis in A549 cells via up-regulating the expression of P53 protein, blocking cell cycle partly at G1 phase, and ultimately activating caspase-3. In contrast, caspase-8 might be irrelevant to EOD-triggered apoptosis. This study indicated that EOD might be a potential chemopreventive agent for lung cancer. The work would encourage us to add more novel compounds to our 'library' of small molecules derived through modern synthetic organic chemistry, and would drive us to determine the proteins that the compounds target.
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Affiliation(s)
- Ai-Ying Du
- Institute of Developmental Biology, School of Life Science, Shandong University, Jinan 250100, China
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11
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Abstract
Spontaneous recovery from extinction is one of the most basic phenomena of Pavlovian conditioning. Although it can be studied by using a variety of designs, some procedures are better than others for identifying the involvement of underlying learning processes. A wide range of different learning mechanisms has been suggested as being engaged by extinction, most of which have implications for the nature of spontaneous recovery. However, despite the centrality of the notion of spontaneous recovery to the understanding of extinction, the empirical literature on its determinants is relatively sparse and quite mixed. Its very ubiquity suggests that spontaneous recovery has multiple sources.
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Affiliation(s)
- Robert A Rescorla
- Department of Psychology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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Westwood NJ. Chemical genetics: how does it function? PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2004; 362:2761-2774. [PMID: 15539369 DOI: 10.1098/rsta.2004.1467] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This article highlights recent successes in the field of chemical genetics. It discusses the challenges inherent in this interdisciplinary research field and focuses on the essential role that the biologically aware synthetic chemist can play.
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Affiliation(s)
- Nicholas J Westwood
- School of Chemistry and Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
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Kelley BP, Lunn MR, Root DE, Flaherty SP, Martino AM, Stockwell BR. A Flexible Data Analysis Tool for Chemical Genetic Screens. ACTA ACUST UNITED AC 2004; 11:1495-503. [PMID: 15556000 DOI: 10.1016/j.chembiol.2004.08.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2004] [Revised: 08/12/2004] [Accepted: 08/31/2004] [Indexed: 12/11/2022]
Abstract
High-throughput assays generate immense quantities of data that require sophisticated data analysis tools. We have created a freely available software tool, SLIMS (Small Laboratory Information Management System), for chemical genetics which facilitates the collection and analysis of large-scale chemical screening data. Compound structures, physical locations, and raw data can be loaded into SLIMS. Raw data from high-throughput assays are normalized using flexible analysis protocols, and systematic spatial errors are automatically identified and corrected. Various computational analyses are performed on tested compounds, and dilution-series data are processed using standard or user-defined algorithms. Finally, published literature associated with active compounds is automatically retrieved from Medline and processed to yield potential mechanisms of actions. SLIMS provides a framework for analyzing high-throughput assay data both as a laboratory information management system and as a platform for experimental analysis.
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Affiliation(s)
- Brian P Kelley
- Department of Biological Sciences, Columbia University, Fairchild Center, MC 2406, 1212 Amsterdam Avenue, New York, NY 10027 USA
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14
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Abstract
Recent advances in cell and molecular biology have generated important tools to probe developmental questions. In addition, new genetic model systems such as Danio rerio now make large-scale vertebrate early developmental mutant screens feasible. Nonetheless, some developmental questions remain difficult to study because of the need for finer temporal, spatial, or tuneable control of gene function within a developmental system. New uses for old teratogens as well as novel chemical modulators of development have begun to fill this void.
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Affiliation(s)
- Jing-Ruey J Yeh
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
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