1
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Naz S, Liu P, Farooq U, Ma H. Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method. Microb Cell Fact 2023; 22:161. [PMID: 37612753 PMCID: PMC10464499 DOI: 10.1186/s12934-023-02178-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023] Open
Abstract
Regulation of amino acid's biosynthetic pathway is of significant importance to maintain homeostasis and cell functions. Amino acids regulate their biosynthetic pathway by end-product feedback inhibition of enzymes catalyzing committed steps of a pathway. Discovery of new feedback resistant enzyme variants to enhance industrial production of amino acids is a key objective in industrial biotechnology. Deregulation of feedback inhibition has been achieved for various enzymes using in vitro and in silico mutagenesis techniques. As enzyme's function, its substrate binding capacity, catalysis activity, regulation and stability are dependent on its structural characteristics, here, we provide detailed structural analysis of all feedback sensitive enzyme targets in amino acid biosynthetic pathways. Current review summarizes information regarding structural characteristics of various enzyme targets and effect of mutations on their structures and functions especially in terms of deregulation of feedback inhibition. Furthermore, applicability of various experimental as well as computational mutagenesis techniques to accomplish feedback resistance has also been discussed in detail to have an insight into various aspects of research work reported in this particular field of study.
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Affiliation(s)
- Sadia Naz
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Pi Liu
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Umar Farooq
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Islamabad, 22060, Pakistan
| | - Hongwu Ma
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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2
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Zeng G, Yu Q, Zhuang R, Zhu H, Shao J, Xi J, Zhang J. Recent Advances and Future Perspectives of Noncompetitive Proteasome Inhibitors. Bioorg Chem 2023; 135:106507. [PMID: 37030106 DOI: 10.1016/j.bioorg.2023.106507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/17/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
The proteasome regulates intracellular processes, maintains biological homeostasis, and has shown great significance in the study of various diseases, such as neurodegenerative diseases, immune-related diseases, and cancer, especially in hematologic malignancies such as multiple myeloma (MM) and mantle cell lymphoma (MCL). All clinically used proteasome inhibitors bind to the active site of the proteasome and thus exhibit a competitive mechanism. The development of resistance and intolerance during treatment drives the search for inhibitors with different mechanisms of action. In this review, we provide an overview of noncompetitive proteasome inhibitors, including their mechanisms of action, function, possible applications, and their advantages and disadvantages compared with competitive inhibitors.
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3
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Serapian SA, Colombo G. Designing Molecular Spanners to Throw in the Protein Networks. Chemistry 2020; 26:4656-4670. [DOI: 10.1002/chem.201904523] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/18/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Stefano A. Serapian
- Department of ChemistryUniversity of Pavia Via Taramelli 12 27100 Pavia Italy
| | - Giorgio Colombo
- Department of ChemistryUniversity of Pavia Via Taramelli 12, 27 100 Pavia Italy
- SCITEC-CNR Via Mario Bianco 9 20131 Milano Italy
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4
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Mutational mimics of allosteric effectors: a genome editing design to validate allosteric drug targets. Sci Rep 2019; 9:9031. [PMID: 31227746 PMCID: PMC6588628 DOI: 10.1038/s41598-019-45202-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/29/2019] [Indexed: 11/08/2022] Open
Abstract
Development of drugs that allosterically regulate enzyme functions to treat disease is a costly venture. Amino acid susbstitutions that mimic allosteric effectors in vitro will identify therapeutic regulatory targets enhancing the likelihood of developing a disease treatment at a reasonable cost. We demonstrate the potential of this approach utilizing human liver pyruvate kinase (hLPYK) as a model. Inhibition of hLPYK was the first desired outcome of this study. We identified individual point mutations that: 1) mimicked allosteric inhibition by alanine, 2) mimicked inhibition by protein phosphorylation, and 3) prevented binding of fructose-1,6-bisphosphate (Fru-1,6-BP). Our second desired outcome was activation of hLPYK. We identified individual point mutations that: 1) prevented hLPYK from binding alanine, the allosteric inhibitor, 2) prevented inhibitory protein phosphorylation, or 3) mimicked allosteric activation by Fru-1,6-BP. Combining the three activating point mutations produced a constitutively activated enzyme that was unresponsive to regulators. Expression of a mutant hLPYK transgene containing these three mutations in a mouse model was not lethal. Thus, mutational mimics of allosteric effectors will be useful to confirm whether allosteric activation of hLPYK will control glycolytic flux in the diabetic liver to reduce hepatic glucose production and, in turn, reduce or prevent hyperglycemia.
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5
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Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE. Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. Chem Rev 2016; 116:6370-90. [PMID: 27074285 PMCID: PMC4901368 DOI: 10.1021/acs.chemrev.5b00631] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
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Allosteric drug development holds
promise for delivering medicines
that are more selective and less toxic than those that target orthosteric
sites. To date, the discovery of allosteric binding sites and lead
compounds has been mostly serendipitous, achieved through high-throughput
screening. Over the past decade, structural data has become more readily
available for larger protein systems and more membrane protein classes
(e.g., GPCRs and ion channels), which are common allosteric drug targets.
In parallel, improved simulation methods now provide better atomistic
understanding of the protein dynamics and cooperative motions that
are critical to allosteric mechanisms. As a result of these advances,
the field of predictive allosteric drug development is now on the
cusp of a new era of rational structure-based computational methods.
Here, we review algorithms that predict allosteric sites based on
sequence data and molecular dynamics simulations, describe tools that
assess the druggability of these pockets, and discuss how Markov state
models and topology analyses provide insight into the relationship
between protein dynamics and allosteric drug binding. In each section,
we first provide an overview of the various method classes before
describing relevant algorithms and software packages.
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Affiliation(s)
- Jeffrey R Wagner
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Christopher T Lee
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Jacob D Durrant
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Robert D Malmstrom
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Victoria A Feher
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
| | - Rommie E Amaro
- Department of Chemistry & Biochemistry and ‡National Biomedical Computation Resource, University of California, San Diego , La Jolla, California 92093, United States
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6
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Azevedo LM, Lansdell TA, Ludwig JR, Mosey RA, Woloch DK, Cogan DP, Patten GP, Kuszpit MR, Fisk JS, Tepe JJ. Inhibition of the human proteasome by imidazoline scaffolds. J Med Chem 2013; 56:5974-8. [PMID: 23789888 DOI: 10.1021/jm400235r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The proteasome has emerged as the primary target for the treatment of multiple myeloma. Unfortunately, nearly all patients develop resistance to competitive-type proteasome inhibitors such as bortezomib. Herein, we describe the optimization of noncompetitive proteasome inhibitors to yield derivatives that exhibit nanomolar potency (compound 49, IC50 130 nM) toward proteasome inhibition and overcome bortezomib resistance. These studies illustrate the feasibility of the development of noncompetitive proteasome inhibitors as additives and/or alternatives to competitive proteasome inhibitors.
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Affiliation(s)
- Lauren M Azevedo
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
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7
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Tzeng SR, Kalodimos CG. Allosteric inhibition through suppression of transient conformational states. Nat Chem Biol 2013; 9:462-5. [DOI: 10.1038/nchembio.1250] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 04/01/2013] [Indexed: 11/09/2022]
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8
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Tertiary and quaternary effects in the allosteric regulation of animal hemoglobins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1860-72. [PMID: 23523886 DOI: 10.1016/j.bbapap.2013.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/07/2013] [Accepted: 03/08/2013] [Indexed: 12/16/2022]
Abstract
In the last decade, protein allostery has experienced a major resurgence, boosted by the extension of the concept to systems of increasing complexity and by its exploitation for the development of drugs. Expansion of the field into new directions has not diminished the key role of hemoglobin as a test molecule for theory and experimental validation of allosteric models. Indeed, the diffusion of hemoglobins in all kingdoms of life and the variety of functions and of quaternary assemblies based on a common tertiary fold indicate that this superfamily of proteins is ideally suited for investigating the physical and molecular basis of allostery and firmly maintains its role as a main player in the field. This review is an attempt to briefly recollect common and different strategies adopted by metazoan hemoglobins, from monomeric molecules to giant complexes, exploiting homotropic and heterotropic allostery to increase their functional dynamic range. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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9
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Lansdell TA, Hurchla MA, Xiang J, Hovde S, Weilbaecher KN, Henry RW, Tepe JJ. Noncompetitive modulation of the proteasome by imidazoline scaffolds overcomes bortezomib resistance and delays MM tumor growth in vivo. ACS Chem Biol 2013. [PMID: 23198928 DOI: 10.1021/cb300568r] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Multiple myeloma (MM) is a malignant disorder of differentiated B-cells for which standard care involves the inhibition of the proteasome. All clinically used proteasome inhibitors, including the chemotherapeutic drug bortezomib, target the catalytic active sites of the proteasome and inhibit protein proteolysis by competing with substrate binding. However, nearly all (~97%) patients become intolerant or resistant to treatments within a few years, after which the average survival time is less than 1 year. We describe herein the inhibition of the human proteasome via a noncompetitive mechanism by the imidazoline scaffold, TCH-13. Consistent with a mechanism distinct from that of competitive inhibitors, TCH-013 acts additively with and overcomes resistance to bortezomib. Importantly, TCH-013 induces apoptosis in a panel of myeloma and leukemia cell lines, but in contrast, normal lymphocytes, primary bone marrow stromal cells (hBMSC), and macrophages are resistant to its cytotoxic effects. TCH-013 was equally effective in blocking MM cell growth in co-cultures of MM cells with hBMSC isolated from CD138 negative bone marrow (BM) samples of MM patients. The cellular activity translated well in vivo where TCH-013 delayed tumor growth in an MM xenograft model to a similar extent as bortezomib.
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Affiliation(s)
| | - Michelle A. Hurchla
- Department of Medicine, Division
of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Jingyu Xiang
- Department of Medicine, Division
of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States
| | | | - Katherine N. Weilbaecher
- Department of Medicine, Division
of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States
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10
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Heise CE, Murray J, Augustyn KE, Bravo B, Chugha P, Cohen F, Giannetti AM, Gibbons P, Hannoush RN, Hearn BR, Jaishankar P, Ly CQ, Shah K, Stanger K, Steffek M, Tang Y, Zhao X, Lewcock JW, Renslo AR, Flygare J, Arkin MR. Mechanistic and structural understanding of uncompetitive inhibitors of caspase-6. PLoS One 2012; 7:e50864. [PMID: 23227217 PMCID: PMC3515450 DOI: 10.1371/journal.pone.0050864] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 10/25/2012] [Indexed: 01/13/2023] Open
Abstract
Inhibition of caspase-6 is a potential therapeutic strategy for some neurodegenerative diseases, but it has been difficult to develop selective inhibitors against caspases. We report the discovery and characterization of a potent inhibitor of caspase-6 that acts by an uncompetitive binding mode that is an unprecedented mechanism of inhibition against this target class. Biochemical assays demonstrate that, while exquisitely selective for caspase-6 over caspase-3 and -7, the compound's inhibitory activity is also dependent on the amino acid sequence and P1' character of the peptide substrate. The crystal structure of the ternary complex of caspase-6, substrate-mimetic and an 11 nM inhibitor reveals the molecular basis of inhibition. The general strategy to develop uncompetitive inhibitors together with the unique mechanism described herein provides a rationale for engineering caspase selectivity.
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Affiliation(s)
- Christopher E. Heise
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California, United States of America
| | - Jeremy Murray
- Department of Structural Biology, Genentech, Inc., South San Francisco, California, United States of America
| | - Katherine E. Augustyn
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Brandon Bravo
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California, United States of America
| | - Preeti Chugha
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Frederick Cohen
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Anthony M. Giannetti
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California, United States of America
| | - Paul Gibbons
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Rami N. Hannoush
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Brian R. Hearn
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Priyadarshini Jaishankar
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Cuong Q. Ly
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Kinjalkumar Shah
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, California, United States of America
| | - Karen Stanger
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Micah Steffek
- Department of Structural Biology, Genentech, Inc., South San Francisco, California, United States of America
| | - Yinyan Tang
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - Xianrui Zhao
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Joseph W. Lewcock
- Department of Neuroscience, Genentech, Inc., South San Francisco, California, United States of America
| | - Adam R. Renslo
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
| | - John Flygare
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Michelle R. Arkin
- Small Molecule Discovery Center, University of California San Francisco, San Francisco, California, United States of America
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11
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Abstract
There is a growing appreciation of the beneficial attributes of allosteric drugs. However, the development of this special class of drugs has in large part been via serendipitous findings from high-throughput screens of drug libraries. Limited success at deliberately identifying allosteric drugs may be due to a focus on enzyme inhibitors, a parallel to the historic focus on competitive inhibitors. In contrast to inhibition, activation of an enzyme by a small molecule can only occur through a limited number of mechanisms, mainly allosteric regulation. Activation of human liver pyruvate kinase (hL-PYK) in an effort to create a glycolytic/gluconeogenic futile cycle is one potential mechanism to counteract hyperglycemia. Using hL-PYK, we demonstrate the potential of drug library screens to identify allosteric-activator drug leads.
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Affiliation(s)
- Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, USA.
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12
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Label-free screening assays: a strategy for finding better drug candidates. Future Med Chem 2010; 2:1703-16. [DOI: 10.4155/fmc.10.246] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The last 10 years have seen advances in automation and high-throughput biochemistry in the drug-discovery arena. However, these advances have not led to improvements in drug-discovery success. Drug programs must find new ways to identify superior compounds. Advances in label-free assay technologies may provide advantages needed for improved drug discovery. In this article, we will discuss high-throughput MS, a technology that allows screening with native substrates and with targets inaccessible to standard assay formats. We will then discuss cell-based label-free biosensors, focusing on the increased information content available when using these platforms. We will conclude with speculation on the future and ways to obtain relevant biological information early in development to ensure the best compounds are promoted to medicinal chemistry campaigns.
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13
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Niswender CM, Johnson KA, Miller NR, Ayala JE, Luo Q, Williams R, Saleh S, Orton D, Weaver CD, Conn PJ. Context-dependent pharmacology exhibited by negative allosteric modulators of metabotropic glutamate receptor 7. Mol Pharmacol 2009; 77:459-68. [PMID: 20026717 DOI: 10.1124/mol.109.058768] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Phenotypic studies of mice lacking metabotropic glutamate receptor subtype 7 (mGluR7) suggest that antagonists of this receptor may be promising for the treatment of central nervous system disorders such as anxiety and depression. Suzuki et al. (J Pharmacol Exp Ther 323:147-156, 2007) recently reported the in vitro characterization of a novel mGluR7 antagonist called 6-(4-methoxyphenyl)-5-methyl-3-(4-pyridinyl)-isoxazolo[ 4,5-c]pyridin-4(5H)-one (MMPIP), which noncompetitively inhibited the activity of orthosteric and allosteric agonists at mGluR7. We describe that MMPIP acts as a noncompetitive antagonist in calcium mobilization assays in cells coexpressing mGluR7 and the promiscuous G protein G alpha(15). Assessment of the activity of a small library of MMPIP-derived compounds using this assay reveals that, despite similar potencies, compounds exhibit differences in negative cooperativity for agonist-mediated calcium mobilization. Examination of the inhibitory activity of MMPIP and analogs using endogenous G(i/o)-coupled assay readouts indicates that the pharmacology of these ligands seems to be context-dependent, and MMPIP exhibits differences in negative cooperativity in certain cellular backgrounds. Electrophysiological studies reveal that, in contrast to the orthosteric antagonist (2S)-2-amino-2-[(1S,2S)-2-carboxyclycloprop-1-yl]-3-(xanth-9-yl) propanoic acid (LY341495), MMPIP is unable to block agonist-mediated responses at the Schaffer collateral-CA1 synapse, a location at which neurotransmission has been shown to be modulated by mGluR7 activity. Thus, MMPIP and related compounds differentially inhibit coupling of mGluR7 in different cellular backgrounds and may not antagonize the coupling of this receptor to native G(i/o) signaling pathways in all cellular contexts. The pharmacology of this compound represents a striking example of the potential for context-dependent blockade of receptor responses by negative allosteric modulators.
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Affiliation(s)
- Colleen M Niswender
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA.
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