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Kornienko M, Bespiatykh D, Gorodnichev R, Abdraimova N, Shitikov E. Transcriptional Landscapes of Herelleviridae Bacteriophages and Staphylococcus aureus during Phage Infection: An Overview. Viruses 2023; 15:1427. [PMID: 37515114 PMCID: PMC10383478 DOI: 10.3390/v15071427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/16/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
The issue of antibiotic resistance in healthcare worldwide has led to a pressing need to explore and develop alternative approaches to combat infectious diseases. Among these methods, phage therapy has emerged as a potential solution to tackle this growing challenge. Virulent phages of the Herelleviridae family, known for their ability to cause lysis of Staphylococcus aureus, a clinically significant pathogen frequently associated with multidrug resistance, have proven to be one of the most effective viruses utilized in phage therapy. In order to utilize phages for therapeutic purposes effectively, a thorough investigation into their physiology and mechanisms of action on infected cells is essential. The use of omics technologies, particularly total RNA sequencing, is a promising approach for analyzing the interaction between phages and their hosts, allowing for the assessment of both the behavior of the phage during infection and the cell's response. This review aims to provide a comprehensive overview of the physiology of the Herelleviridae family, utilizing existing analyses of their total phage transcriptomes. Additionally, it sheds light on the changes that occur in the metabolism of S. aureus when infected with virulent bacteriophages, contributing to a deeper understanding of the phage-host interaction.
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Affiliation(s)
- Maria Kornienko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
| | - Dmitry Bespiatykh
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
| | - Roman Gorodnichev
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
| | - Narina Abdraimova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
| | - Egor Shitikov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency Medicine, Moscow 119435, Russia
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Kornienko M, Fisunov G, Bespiatykh D, Kuptsov N, Gorodnichev R, Klimina K, Kulikov E, Ilina E, Letarov A, Shitikov E. Transcriptional Landscape of Staphylococcus aureus Kayvirus Bacteriophage vB_SauM-515A1. Viruses 2020; 12:E1320. [PMID: 33213043 PMCID: PMC7698491 DOI: 10.3390/v12111320] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/09/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022] Open
Abstract
The Twort-like myoviruses (Kayvirus genus) of S. aureus are promising agents for bacteriophage therapy due to a broad host range and high killing activity against clinical isolates. This work improves the current understanding of the phage infection physiology by transcriptome analysis. The expression profiles of a typical member of the Kayvirus genus (vB_SauM-515A1) were obtained at three time-points post-infection using RNA sequencing. A total of 35 transcription units comprising 238 ORFs were established. The sequences for 58 early and 12 late promoters were identified in the phage genome. The early promoters represent the strong sigma-70 promoters consensus sequence and control the host-dependent expression of 26 transcription units (81% of genes). The late promoters exclusively controlled the expression of four transcription units, while the transcription of the other five units was directed by both types of promoters. The characteristic features of late promoters were long -10 box of TGTTATATTA consensus sequence and the absence of -35 boxes. The data obtained are also of general interest, demonstrating a strategy of the phage genome expression with a broad overlap of the early and late transcription phases without any middle transcription, which is unusual for the large phage genomes (>100 kbp).
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Affiliation(s)
- Maria Kornienko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Gleb Fisunov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Dmitry Bespiatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Nikita Kuptsov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Roman Gorodnichev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Ksenia Klimina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Eugene Kulikov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, 117312 Moscow, Russia; (E.K.); (A.L.)
| | - Elena Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
| | - Andrey Letarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, 117312 Moscow, Russia; (E.K.); (A.L.)
| | - Egor Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (G.F.); (D.B.); (N.K.); (R.G.); (K.K.); (E.I.); (E.S.)
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Kornienko M, Kuptsov N, Gorodnichev R, Bespiatykh D, Guliaev A, Letarova M, Kulikov E, Veselovsky V, Malakhova M, Letarov A, Ilina E, Shitikov E. Contribution of Podoviridae and Myoviridae bacteriophages to the effectiveness of anti-staphylococcal therapeutic cocktails. Sci Rep 2020; 10:18612. [PMID: 33122703 PMCID: PMC7596081 DOI: 10.1038/s41598-020-75637-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023] Open
Abstract
Bacteriophage therapy is considered one of the most promising therapeutic approaches against multi-drug resistant bacterial infections. Infections caused by Staphylococcus aureus are very efficiently controlled with therapeutic bacteriophage cocktails, containing a number of individual phages infecting a majority of known pathogenic S. aureus strains. We assessed the contribution of individual bacteriophages comprising a therapeutic bacteriophage cocktail against S. aureus in order to optimize its composition. Two lytic bacteriophages vB_SauM-515A1 (Myoviridae) and vB_SauP-436A (Podoviridae) were isolated from the commercial therapeutic cocktail produced by Microgen (Russia). Host ranges of the phages were established on the panel of 75 S. aureus strains. Phage vB_SauM-515A1 lysed 85.3% and vB_SauP-436A lysed 68.0% of the strains, however, vB_SauP-436A was active against four strains resistant to vB_SauM-515A1, as well as to the therapeutic cocktail per se. Suboptimal results of the therapeutic cocktail application were due to extremely low vB_SauP-436A1 content in this composition. Optimization of the phage titers led to an increase in overall cocktail efficiency. Thus, one of the effective ways to optimize the phage cocktails design was demonstrated and realized by using bacteriophages of different families and lytic spectra.
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Affiliation(s)
- Maria Kornienko
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia.
| | - Nikita Kuptsov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Roman Gorodnichev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Dmitry Bespiatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Andrei Guliaev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Maria Letarova
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Eugene Kulikov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Vladimir Veselovsky
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Maya Malakhova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Andrey Letarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Elena Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Egor Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
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Forster AB, Abeywickrema P, Bunda J, Cox CD, Cabalu TD, Egbertson M, Fay J, Getty K, Hall D, Kornienko M, Lu J, Parthasarathy G, Reid J, Sharma S, Shipe WD, Smith SM, Soisson S, Stachel SJ, Su HP, Wang D, Berger R. The identification of a novel lead class for phosphodiesterase 2 inhibition by fragment-based drug design. Bioorg Med Chem Lett 2017; 27:5167-5171. [DOI: 10.1016/j.bmcl.2017.10.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/18/2017] [Accepted: 10/22/2017] [Indexed: 01/25/2023]
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Novik A, Baldueva I, Protsenko S, Nehaeva T, Danolova A, Pipia N, Olisova N, Kornienko M, Danilova T. Adjuvant therapy with autologous dendritic cell (DC) vaccine based on cancer-testis antigens (CaTeVac) in melanoma patients. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx376.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Lu J, Byrne N, Wang J, Bricogne G, Brown FK, Chobanian HR, Colletti SL, Di Salvo J, Thomas-Fowlkes B, Guo Y, Hall DL, Hadix J, Hastings NB, Hermes JD, Ho T, Howard AD, Josien H, Kornienko M, Lumb KJ, Miller MW, Patel SB, Pio B, Plummer CW, Sherborne BS, Sheth P, Souza S, Tummala S, Vonrhein C, Webb M, Allen SJ, Johnston JM, Weinglass AB, Sharma S, Soisson SM. Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40. Nat Struct Mol Biol 2017; 24:570-577. [PMID: 28581512 DOI: 10.1038/nsmb.3417] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 05/08/2017] [Indexed: 12/19/2022]
Abstract
Clinical studies indicate that partial agonists of the G-protein-coupled, free fatty acid receptor 1 GPR40 enhance glucose-dependent insulin secretion and represent a potential mechanism for the treatment of type 2 diabetes mellitus. Full allosteric agonists (AgoPAMs) of GPR40 bind to a site distinct from partial agonists and can provide additional efficacy. We report the 3.2-Å crystal structure of human GPR40 (hGPR40) in complex with both the partial agonist MK-8666 and an AgoPAM, which exposes a novel lipid-facing AgoPAM-binding pocket outside the transmembrane helical bundle. Comparison with an additional 2.2-Å structure of the hGPR40-MK-8666 binary complex reveals an induced-fit conformational coupling between the partial agonist and AgoPAM binding sites, involving rearrangements of the transmembrane helices 4 and 5 (TM4 and TM5) and transition of the intracellular loop 2 (ICL2) into a short helix. These conformational changes likely prime GPR40 to a more active-like state and explain the binding cooperativity between these ligands.
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Affiliation(s)
- Jun Lu
- Department of Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Noel Byrne
- Department of Screening and Protein Science, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - John Wang
- Department of In vitro Pharmacology, Merck Research Laboratories, West Point, Pennsylvania, USA
| | | | - Frank K Brown
- Department of Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Harry R Chobanian
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Steven L Colletti
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Jerry Di Salvo
- Department of In vitro Pharmacology, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Brande Thomas-Fowlkes
- Department of In vitro Pharmacology, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Yan Guo
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Dawn L Hall
- Department of Screening and Protein Science, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Jennifer Hadix
- Department of Screening and Protein Science, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Nicholas B Hastings
- Department of In vitro Pharmacology, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Jeffrey D Hermes
- Department of Screening and Protein Science, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Thu Ho
- Department of Screening and Protein Science, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Andrew D Howard
- Department of Cardiometabolic Disease, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Hubert Josien
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Maria Kornienko
- Department of Screening and Protein Science, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Kevin J Lumb
- Department of Screening and Protein Science, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Michael W Miller
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Sangita B Patel
- Department of Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Barbara Pio
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Christopher W Plummer
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Bradley S Sherborne
- Department of Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Payal Sheth
- Department of In vitro Pharmacology, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Sarah Souza
- Department of In vitro Pharmacology, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Srivanya Tummala
- Department of Screening and Protein Science, Merck Research Laboratories, West Point, Pennsylvania, USA
| | | | - Maria Webb
- Department of In vitro Pharmacology, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Samantha J Allen
- Department of Screening and Protein Science, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Jennifer M Johnston
- Department of Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Adam B Weinglass
- Department of In vitro Pharmacology, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Sujata Sharma
- Department of Screening and Protein Science, Merck Research Laboratories, West Point, Pennsylvania, USA
| | - Stephen M Soisson
- Department of Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania, USA
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7
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Elsen NL, Patel SB, Ford RE, Hall DL, Hess F, Kandula H, Kornienko M, Reid J, Selnick H, Shipman JM, Sharma S, Lumb KJ, Soisson SM, Klein DJ. Insights into activity and inhibition from the crystal structure of human O-GlcNAcase. Nat Chem Biol 2017; 13:613-615. [PMID: 28346407 DOI: 10.1038/nchembio.2357] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/09/2017] [Indexed: 12/13/2022]
Abstract
O-GlcNAc hydrolase (OGA) catalyzes removal of βα-linked N-acetyl-D-glucosamine from serine and threonine residues. We report crystal structures of Homo sapiens OGA catalytic domain in apo and inhibited states, revealing a flexible dimer that displays three unique conformations and is characterized by subdomain α-helix swapping. These results identify new structural features of the substrate-binding groove adjacent to the catalytic site and open new opportunities for structural, mechanistic and drug discovery activities.
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Affiliation(s)
- Nathaniel L Elsen
- Screening and Protein Sciences, MRL, Merck &Co., Inc., West Point, Pennsylvania, USA
| | - Sangita B Patel
- Structural Chemistry, MRL, Merck &Co., Inc., West Point, Pennsylvania, USA
| | - Rachael E Ford
- Screening and Protein Sciences, MRL, Merck &Co., Inc., West Point, Pennsylvania, USA
| | - Dawn L Hall
- Screening and Protein Sciences, MRL, Merck &Co., Inc., West Point, Pennsylvania, USA
| | - Fred Hess
- Department of Neurobiology, MRL, Merck &Co., Inc., West Point, Pennsylvania, USA
| | - Hari Kandula
- Screening and Protein Sciences, MRL, Merck &Co., Inc., West Point, Pennsylvania, USA
| | - Maria Kornienko
- Screening and Protein Sciences, MRL, Merck &Co., Inc., West Point, Pennsylvania, USA
| | - John Reid
- Structural Chemistry, MRL, Merck &Co., Inc., West Point, Pennsylvania, USA
| | - Harold Selnick
- Discovery Chemistry, MRL, Merck &Co., Inc., West Point, Pennsylvania, USA
| | - Jennifer M Shipman
- Screening and Protein Sciences, MRL, Merck &Co., Inc., West Point, Pennsylvania, USA
| | - Sujata Sharma
- Screening and Protein Sciences, MRL, Merck &Co., Inc., West Point, Pennsylvania, USA
| | - Kevin J Lumb
- Screening and Protein Sciences, MRL, Merck &Co., Inc., West Point, Pennsylvania, USA
| | - Stephen M Soisson
- Structural Chemistry, MRL, Merck &Co., Inc., West Point, Pennsylvania, USA
| | - Daniel J Klein
- Structural Chemistry, MRL, Merck &Co., Inc., West Point, Pennsylvania, USA
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8
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Kornienko M, Ilina E, Lubasovskaya L, Priputnevich T, Falova O, Sukhikh G, Govorun V. Analysis of nosocomial Staphylococcus haemolyticus by MLST and MALDI-TOF mass spectrometry. Infection, Genetics and Evolution 2016; 39:99-105. [DOI: 10.1016/j.meegid.2015.12.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/30/2015] [Accepted: 12/18/2015] [Indexed: 11/25/2022]
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9
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Kutilek VD, Andrews CL, Richards MP, Xu Z, Sun T, Chen Y, Hashke A, Smotrov N, Fernandez R, Nickbarg EB, Chamberlin C, Sauvagnat B, Curran PJ, Boinay R, Saradjian P, Allen SJ, Byrne N, Elsen NL, Ford RE, Hall DL, Kornienko M, Rickert KW, Sharma S, Shipman JM, Lumb KJ, Coleman K, Dandliker PJ, Kariv I, Beutel B. Integration of Affinity Selection-Mass Spectrometry and Functional Cell-Based Assays to Rapidly Triage Druggable Target Space within the NF-κB Pathway. ACTA ACUST UNITED AC 2016; 21:608-19. [PMID: 26969322 DOI: 10.1177/1087057116637353] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/15/2016] [Indexed: 11/15/2022]
Abstract
The primary objective of early drug discovery is to associate druggable target space with a desired phenotype. The inability to efficiently associate these often leads to failure early in the drug discovery process. In this proof-of-concept study, the most tractable starting points for drug discovery within the NF-κB pathway model system were identified by integrating affinity selection-mass spectrometry (AS-MS) with functional cellular assays. The AS-MS platform Automated Ligand Identification System (ALIS) was used to rapidly screen 15 NF-κB proteins in parallel against large-compound libraries. ALIS identified 382 target-selective compounds binding to 14 of the 15 proteins. Without any chemical optimization, 22 of the 382 target-selective compounds exhibited a cellular phenotype consistent with the respective target associated in ALIS. Further studies on structurally related compounds distinguished two chemical series that exhibited a preliminary structure-activity relationship and confirmed target-driven cellular activity to NF-κB1/p105 and TRAF5, respectively. These two series represent new drug discovery opportunities for chemical optimization. The results described herein demonstrate the power of combining ALIS with cell functional assays in a high-throughput, target-based approach to determine the most tractable drug discovery opportunities within a pathway.
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Affiliation(s)
- Victoria D Kutilek
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Christine L Andrews
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Matthew P Richards
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Zangwei Xu
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Tianxiao Sun
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Yiping Chen
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Andrew Hashke
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Nadya Smotrov
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Rafael Fernandez
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Elliott B Nickbarg
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Chad Chamberlin
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Berengere Sauvagnat
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Patrick J Curran
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Ryan Boinay
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Peter Saradjian
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Samantha J Allen
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Noel Byrne
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Nathaniel L Elsen
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA Current address: AbbVie, North Chicago, IL USA
| | - Rachael E Ford
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Dawn L Hall
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Maria Kornienko
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Keith W Rickert
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA Current address: Medimmune, Gaithersburg, MD, USA
| | - Sujata Sharma
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Jennifer M Shipman
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Kevin J Lumb
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Kevin Coleman
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA Current address: Arvinas, New Haven, CT, USA
| | - Peter J Dandliker
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Ilona Kariv
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
| | - Bruce Beutel
- Department of Pharmacology, Screening and Protein Sciences, Merck & Co, Kenilworth, NJ, USA
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10
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Clayton GM, Klein DJ, Rickert KW, Patel SB, Kornienko M, Zugay-Murphy J, Reid JC, Tummala S, Sharma S, Singh SB, Miesel L, Lumb KJ, Soisson SM. Structure of the bacterial deacetylase LpxC bound to the nucleotide reaction product reveals mechanisms of oxyanion stabilization and proton transfer. J Biol Chem 2013; 288:34073-34080. [PMID: 24108127 DOI: 10.1074/jbc.m113.513028] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The emergence of antibiotic-resistant strains of pathogenic bacteria is an increasing threat to global health that underscores an urgent need for an expanded antibacterial armamentarium. Gram-negative bacteria, such as Escherichia coli, have become increasingly important clinical pathogens with limited treatment options. This is due in part to their lipopolysaccharide (LPS) outer membrane components, which dually serve as endotoxins while also protecting Gram-negative bacteria from antibiotic entry. The LpxC enzyme catalyzes the committed step of LPS biosynthesis, making LpxC a promising target for new antibacterials. Here, we present the first structure of an LpxC enzyme in complex with the deacetylation reaction product, UDP-(3-O-(R-3-hydroxymyristoyl))-glucosamine. These studies provide valuable insight into recognition of substrates and products by LpxC and a platform for structure-guided drug discovery of broad spectrum Gram-negative antibiotics.
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Affiliation(s)
- Gina M Clayton
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Daniel J Klein
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Keith W Rickert
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Sangita B Patel
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Maria Kornienko
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Joan Zugay-Murphy
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - John C Reid
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Srivanya Tummala
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Sujata Sharma
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Sheo B Singh
- Discovery Chemistry, Merck Research Laboratories, Kenilworth, New Jersey 07033
| | - Lynn Miesel
- Infectious Diseases, Merck Research Laboratories, Kenilworth, New Jersey 07033
| | - Kevin J Lumb
- Screening and Protein Sciences, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Stephen M Soisson
- Global Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486.
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Rickert KW, Patel SB, Allison TJ, Byrne NJ, Darke PL, Ford RE, Guerin DJ, Hall DL, Kornienko M, Lu J, Munshi SK, Reid JC, Shipman JM, Stanton EF, Wilson KJ, Young JR, Soisson SM, Lumb KJ. Structural basis for selective small molecule kinase inhibition of activated c-Met. J Biol Chem 2011; 286:11218-25. [PMID: 21247903 DOI: 10.1074/jbc.m110.204404] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The receptor tyrosine kinase c-Met is implicated in oncogenesis and is the target for several small molecule and biologic agents in clinical trials for the treatment of cancer. Binding of the hepatocyte growth factor to the cell surface receptor of c-Met induces activation via autophosphorylation of the kinase domain. Here we describe the structural basis of c-Met activation upon autophosphorylation and the selective small molecule inhibiton of autophosphorylated c-Met. MK-2461 is a potent c-Met inhibitor that is selective for the phosphorylated state of the enzyme. Compound 1 is an MK-2461 analog with a 20-fold enthalpy-driven preference for the autophosphorylated over unphosphorylated c-Met kinase domain. The crystal structure of the unbound kinase domain phosphorylated at Tyr-1234 and Tyr-1235 shows that activation loop phosphorylation leads to the ejection and disorder of the activation loop and rearrangement of helix αC and the G loop to generate a viable active site. Helix αC adopts a orientation different from that seen in activation loop mutants. The crystal structure of the complex formed by the autophosphorylated c-Met kinase domain and compound 1 reveals a significant induced fit conformational change of the G loop and ordering of the activation loop, explaining the selectivity of compound 1 for the autophosphorylated state. The results highlight the role of structural plasticity within the kinase domain in imparting the specificity of ligand binding and provide the framework for structure-guided design of activated c-Met inhibitors.
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Affiliation(s)
- Keith W Rickert
- Global Structural Biology, Merck Research Laboratories, West Point, Pennsylvania 19486, USA
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12
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Ikuta M, Kornienko M, Byrne N, Reid JC, Mizuarai S, Kotani H, Munshi SK. Crystal structures of the N-terminal kinase domain of human RSK1 bound to three different ligands: Implications for the design of RSK1 specific inhibitors. Protein Sci 2007; 16:2626-35. [PMID: 17965187 DOI: 10.1110/ps.073123707] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The p90 ribosomal S6 kinases (RSKs) also known as MAPKAP-Ks are serine/threonine protein kinases that are activated by ERK or PDK1 and act as downstream effectors of mitogen-activated protein kinase (MAPK). RSK1, a member of the RSK family, contains two distinct kinase domains in a single polypeptide chain, the regulatory C-terminal kinase domain (CTKD) and the catalytic N-terminal kinase domain (NTKD). Autophosphorylation of the CTKD leads to activation of the NTKD that subsequently phosphorylates downstream substrates. Here we report the crystal structures of the unactivated RSK1 NTKD bound to different ligands at 2.0 A resolution. The activation loop and helix alphaC, key regulatory elements of kinase function, are disordered. The DFG motif of the inactive RSK1 adopts an "active-like" conformation. The beta-PO(4) group in the AMP-PCP complex adopts a unique conformation that may contribute to inactivity of the enzyme. Structures of RSK1 ligand complexes offer insights into the design of novel anticancer agents and into the regulation of the catalytic activity of RSKs.
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Affiliation(s)
- Mari Ikuta
- Department of Structural Biology, Merck Research Laboratories, West Point, Pennsylvania 19486, USA. mari_ikuta@.merck.com
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13
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Kornienko M, Montalvo A, Carpenter BE, Lenard M, Abeywickrema P, Hall DL, Darke PL, Kuo LC. Protein expression plasmids produced rapidly: streamlining cloning protocols and robotic handling. Assay Drug Dev Technol 2006; 3:661-74. [PMID: 16438661 DOI: 10.1089/adt.2005.3.661] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As many processes in the preclinical drug discovery process become highly parallel, the need to also produce a large number of different proteins in parallel has become acute, such as for protein crystallization and activity screening. In turn, the requisite DNA constructions to produce these proteins must now be done at a rate that requires automated cloning procedures, each with an intrinsic low failure probability per sample. The high-throughput cloning solutions presented here achieve production of 192 different expression plasmids at a success rate of greater than 95% of the targeted open reading frames. Time for completion of the set by one person is reduced to approximately 11 working days, starting with polymerase chain reactions for a number of source clones and ending with purified expression plasmids. Achievement of this throughput utilizes the following: (1) the Beckman Coulter (Fullerton, CA) Biomek FX liquid handler for most manipulations, (2) Gateway cloning technology (Invitrogen Corp., Carlsbad, CA), and (3) computer programs designed for parallel processing of all sample information, including primer design and the resulting DNA and protein sequence assembly. Exemplary data are presented for discovery of a form of the Rho-kinase that crystallizes (ROCK2).
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Affiliation(s)
- Maria Kornienko
- Department of Structural Biology, Merck Research Laboratories, West Point, PA 19486, USA.
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14
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Bell IM, Stirdivant SM, Ahern J, Culberson JC, Darke PL, Dinsmore CJ, Drakas RA, Gallicchio SN, Graham SL, Heimbrook DC, Hall DL, Hua J, Kett NR, Kim AS, Kornienko M, Kuo LC, Munshi SK, Quigley AG, Reid JC, Trotter BW, Waxman LH, Williams TM, Zartman CB. Biochemical and Structural Characterization of a Novel Class of Inhibitors of the Type 1 Insulin-like Growth Factor and Insulin Receptor Kinases. Biochemistry 2005; 44:9430-40. [PMID: 15996097 DOI: 10.1021/bi0500628] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The type 1 insulin-like growth factor receptor (IGF-1R) is often overexpressed on tumor cells and is believed to play an important role in anchorage-independent proliferation. Additionally, cell culture studies have indicated that IGF-1R confers increased resistance to apoptosis caused by radiation or chemotherapeutic agents. Thus, inhibitors of the intracellular kinase domain of this receptor may have utility for the clinical treatment of cancer. As part of an effort to develop clinically useful inhibitors of IGF-1R kinase, a novel class of pyrrole-5-carboxaldehyde compounds was investigated. The compounds exhibited selectivity against the closely related insulin receptor kinase intrinsically and in cell-based assays. The inhibitors formed a reversible, covalent adduct at the kinase active site, and treatment of such adducts with sodium borohydride irreversibly inactivated the enzyme. Analysis of a tryptic digest of a covalently modified IGF-1R kinase fragment revealed that the active site Lys1003 had been reductively alkylated with the aldehyde inhibitor. Reductive alkylation of the insulin receptor kinase with one of these inhibitors led to a similarly inactivated enzyme which was examined by X-ray crystallography. The crystal structure confirmed the modification of the active site lysine side chain and revealed details of the key interactions between the inhibitor and enzyme.
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Affiliation(s)
- Ian M Bell
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, USA.
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Munshi S, Hall DL, Kornienko M, Darke PL, Kuo LC. Structure of apo, unactivated insulin-like growth factor-1 receptor kinase at 1.5 Å resolution. Acta Crystallogr D Biol Crystallogr 2003; 59:1725-30. [PMID: 14501110 DOI: 10.1107/s0907444903015415] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2003] [Accepted: 07/11/2003] [Indexed: 11/11/2022]
Abstract
The crystal structure of the wild-type unactivated kinase domain (IGFRK-0P) of insulin-like growth factor-1 receptor has been reported previously at 2.7 A resolution [Munshi et al. (2002), J. Biol. Chem. 277, 38797-38802]. In order to obtain a high-resolution structure, a number of variants of IGFRK-0P were prepared and screened for crystallization. A double mutant with E1067A and E1069A substitutions within the kinase-insert region resulted in crystals that diffracted to 1.5 A resolution. Overall, the structure of the mutant IGFRK-0P is similar to that of the wild-type IGFRK-0P structure, with the exception of the previously disordered kinase-insert region in the wild type having become fixed. In addition, amino-acid residues 947-952 at the N-terminus are well defined in the mutant structure. The monomeric protein structure is folded into two lobes connected by a hinge region, with the catalytic center situated at the interface of the two lobes. Two molecules of IGFRK-0P in the asymmetric unit are associated as a dimer and two different types of dimers with their ATP-binding clefts either facing towards or away from each other are observed. The current refined model consists of a dimer and 635 water molecules.
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Affiliation(s)
- Sanjeev Munshi
- Department of Structural Biology, Merck Research Laboratories, West Point, PA 19486, USA.
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Munshi S, Kornienko M, Hall DL, Reid JC, Waxman L, Stirdivant SM, Darke PL, Kuo LC. Crystal structure of the Apo, unactivated insulin-like growth factor-1 receptor kinase. Implication for inhibitor specificity. J Biol Chem 2002; 277:38797-802. [PMID: 12138114 DOI: 10.1074/jbc.m205580200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The x-ray structure of the unactivated kinase domain of insulin-like growth factor-1 receptor (IGFRK-0P) is reported here at 2.7 A resolution. IGFRK-0P is composed of two lobes connected by a hinge region. The N-terminal lobe of the kinase is a twisted beta-sheet flanked by a single helix, and the C-terminal lobe comprises eight alpha-helices and four short beta-strands. The ATP binding pocket and the catalytic center reside at the interface of the two lobes. Despite the overall similarity to other receptor tyrosine kinases, three notable conformational modifications are observed: 1) this kinase adopts a more closed structure, with its two lobes rotated further toward each other; 2) the conformation of the proximal end of the activation loop (residues 1121-1129) is different; 3) the orientation of the nucleotide-binding loop is altered. Collectively, these alterations lead to a different ATP-binding pocket that might impact on inhibitor designs for IGFRK-0P. Two molecules of IGFRK-0P are seen in the asymmetric unit; they are associated as a dimer with their ATP binding clefts facing each other. The ordered N terminus of one monomer approaches the active site of the other, suggesting that the juxtamembrane region of one molecule could come into close proximity to the active site of the other.
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Affiliation(s)
- Sanjeev Munshi
- Department of Structural Biology, Merck Research Laboratories, West Point, Pennsylvania 19486, USA
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