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Bungard CJ, Williams PD, Ballard JE, Bennett DJ, Beaulieu C, Bahnck-Teets C, Carroll SS, Chang RK, Dubost DC, Fay JF, Diamond TL, Greshock TJ, Hao L, Holloway MK, Felock PJ, Gesell JJ, Su HP, Manikowski JJ, McKay DJ, Miller M, Min X, Molinaro C, Moradei OM, Nantermet PG, Nadeau C, Sanchez RI, Satyanarayana T, Shipe WD, Singh SK, Truong VL, Vijayasaradhi S, Wiscount CM, Vacca JP, Crane SN, McCauley JA. Discovery of MK-8718, an HIV Protease Inhibitor Containing a Novel Morpholine Aspartate Binding Group. ACS Med Chem Lett 2016; 7:702-7. [PMID: 27437081 DOI: 10.1021/acsmedchemlett.6b00135] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 03/30/2016] [Accepted: 05/09/2016] [Indexed: 12/18/2022] Open
Abstract
A novel HIV protease inhibitor was designed using a morpholine core as the aspartate binding group. Analysis of the crystal structure of the initial lead bound to HIV protease enabled optimization of enzyme potency and antiviral activity. This afforded a series of potent orally bioavailable inhibitors of which MK-8718 was identified as a compound with a favorable overall profile.
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Affiliation(s)
- Christopher J. Bungard
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Peter D. Williams
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Jeanine E. Ballard
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - David J. Bennett
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Christian Beaulieu
- Merck Frosst Centre for Therapeutic Research, 16711 TransCanada Highway, Kirkland, Quebec H9H 3L1, Canada
| | - Carolyn Bahnck-Teets
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Steve S. Carroll
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Ronald K. Chang
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - David C. Dubost
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - John F. Fay
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Tracy L. Diamond
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Thomas J. Greshock
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Li Hao
- Albany Molecular Research Singapore Research Center, 61 Science Park Road #05-01, The Galen Singapore
Science Park II, Singapore 117525
| | - M. Katharine Holloway
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | | | - Jennifer J. Gesell
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Hua-Poo Su
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Jesse J. Manikowski
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Daniel J. McKay
- Merck Frosst Centre for Therapeutic Research, 16711 TransCanada Highway, Kirkland, Quebec H9H 3L1, Canada
| | - Mike Miller
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Xu Min
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Carmela Molinaro
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Oscar M. Moradei
- Merck Frosst Centre for Therapeutic Research, 16711 TransCanada Highway, Kirkland, Quebec H9H 3L1, Canada
| | - Philippe G. Nantermet
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Christian Nadeau
- Merck Frosst Centre for Therapeutic Research, 16711 TransCanada Highway, Kirkland, Quebec H9H 3L1, Canada
| | - Rosa I. Sanchez
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Tummanapalli Satyanarayana
- Albany Molecular Research Singapore Research Center, 61 Science Park Road #05-01, The Galen Singapore
Science Park II, Singapore 117525
| | - William D. Shipe
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Sanjay K. Singh
- Albany Molecular Research Singapore Research Center, 61 Science Park Road #05-01, The Galen Singapore
Science Park II, Singapore 117525
| | - Vouy Linh Truong
- Merck Frosst Centre for Therapeutic Research, 16711 TransCanada Highway, Kirkland, Quebec H9H 3L1, Canada
| | - Sivalenka Vijayasaradhi
- Albany Molecular Research Singapore Research Center, 61 Science Park Road #05-01, The Galen Singapore
Science Park II, Singapore 117525
| | - Catherine M. Wiscount
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
| | - Joseph P. Vacca
- Merck Frosst Centre for Therapeutic Research, 16711 TransCanada Highway, Kirkland, Quebec H9H 3L1, Canada
| | - Sheldon N. Crane
- Merck Frosst Centre for Therapeutic Research, 16711 TransCanada Highway, Kirkland, Quebec H9H 3L1, Canada
| | - John A. McCauley
- Merck Research Laboratories, 770 Sumneytown Pike, PO Box 4, West Point, Pennsylvania 19486, United States
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Salowe SP, Zhang L, Zokian HJ, Gesell JJ, Zink DL, Wiltsie J, Ai X, Kavana M, Pinto S. In Vitro Assays for the Discovery of PCSK9 Autoprocessing Inhibitors. ACTA ACUST UNITED AC 2016; 21:1034-1041. [DOI: 10.1177/1087057116657312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PCSK9 plays a significant role in regulating low-density lipoprotein (LDL) cholesterol levels and has become an important drug target for treating hypercholesterolemia. Although a member of the serine protease family, PCSK9 only catalyzes a single reaction, the autocleavage of its prodomain. The maturation of the proprotein is an essential prerequisite for the secretion of PCSK9 to the extracellular space where it binds the LDL receptor and targets it for degradation. We have found that a construct of proPCSK9 where the C-terminal domain has been truncated has sufficient stability to be expressed and purified from Escherichia coli for the in vitro study of autoprocessing. Using automated Western analysis, we demonstrate that autoprocessing exhibits the anticipated first-order kinetics. A high-throughput time-resolved fluorescence resonance energy transfer assay for autocleavage has been developed using a PCSK9 monoclonal antibody that is sensitive to the conformational changes that occur upon maturation of the proprotein. Kinetic theory has been developed that describes the behavior of both reversible and irreversible inhibitors of autocleavage. The analysis of an irreversible lactone inhibitor validates the expected relationship between potency and the reaction end point. An orthogonal liquid chromatography–mass spectrometry assay has also been implemented for the confirmation of hits from the antibody-based assays.
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Affiliation(s)
- Scott P. Salowe
- Department of In Vitro Pharmacology, Merck Research Laboratories, Kenilworth, NJ, USA
| | - Lei Zhang
- Department of In Vitro Pharmacology, Merck Research Laboratories, Kenilworth, NJ, USA
| | - Hratch J. Zokian
- Department of In Vitro Pharmacology, Merck Research Laboratories, Kenilworth, NJ, USA
| | - Jennifer J. Gesell
- Department of In Vitro Pharmacology, Merck Research Laboratories, Kenilworth, NJ, USA
- Current address: Janssen Research & Development LLC, Spring House, PA, USA
| | - Deborah L. Zink
- Department of In Vitro Pharmacology, Merck Research Laboratories, Kenilworth, NJ, USA
| | - Judyann Wiltsie
- Department of In Vitro Pharmacology, Merck Research Laboratories, Kenilworth, NJ, USA
| | - Xi Ai
- Department of In Vitro Pharmacology, Merck Research Laboratories, Kenilworth, NJ, USA
| | - Michael Kavana
- Department of In Vitro Pharmacology, Merck Research Laboratories, Kenilworth, NJ, USA
| | - Shirly Pinto
- Department of Cardiometabolic Diseases, Merck Research Laboratories, Kenilworth, NJ, USA
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Liu D, Wang YS, Gesell JJ, Wyss DF. Solution structure and backbone dynamics of an engineered arginine-rich subdomain 2 of the hepatitis C virus NS3 RNA helicase. J Mol Biol 2001; 314:543-61. [PMID: 11846566 DOI: 10.1006/jmbi.2001.5146] [Citation(s) in RCA: 14] [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: 11/22/2022]
Abstract
The NS3 protein of the hepatitis C virus (HCV) is a 631 amino acid residue bifunctional enzyme with a serine protease localized to the N-terminal 181 residues and an RNA helicase located in the C-terminal 450 residues. The HCV NS3 RNA helicase consists of three well-defined subdomains which all contribute to its helicase activity. The second subdomain of the HCV helicase is flexibly linked to the remainder of the NS3 protein and could undergo rigid-body movements during the unwinding of double-stranded RNA. It also contains several motifs that are implicated in RNA binding and in coupling NTP hydrolysis to nucleic acid unwinding and translocation. As part of our efforts to use NMR techniques to assist in deciphering the enzyme's structure-function relationships and developing specific small molecule inhibitors, we have determined the solution structure of an engineered subdomain 2 of the NS3 RNA helicase of HCV, d(2Delta)-HCVh, and studied the backbone dynamics of this protein by (15)N-relaxation experiments using a model-free approach. The NMR studies on this 142-residue construct reveal that overall subdomain 2 of the HCV helicase is globular and well structured in solution even in the absence of the remaining parts of the NS3 protein. Its solution structure is very similar to the corresponding parts in the X-ray structures of the HCV NS3 helicase domain and intact bifunctional HCV NS3 protein. Slow hydrogen-deuterium exchange rates map to a well-structured, stable hydrophobic core region away from the subdomain interfaces. In contrast, the regions facing the subdomain interfaces in the HCV NS3 helicase domain are less well structured in d(2Delta)-HCVh, show fast hydrogen-deuterium exchange rates, and the analysis of the dynamic properties of d(2Delta)-HCVh reveals that these regions of the protein show distinct dynamical features. In particular, residues in motif V, which may be involved in transducing allosteric effects of nucleotide binding and hydrolysis on RNA binding, exhibit slow conformational exchange on the milli- to microsecond time-scale. The intrinsic conformational flexibility of this loop region may facilitate conformational changes required for helicase function.
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Affiliation(s)
- D Liu
- Department of Structural Chemistry, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
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Gesell JJ, Liu D, Madison VS, Hesson T, Wang YS, Weber PC, Wyss DF. Design, high-level expression, purification and characterization of soluble fragments of the hepatitis C virus NS3 RNA helicase suitable for NMR-based drug discovery methods and mechanistic studies. Protein Eng 2001; 14:573-82. [PMID: 11579226 DOI: 10.1093/protein/14.8.573] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
RNA helicases represent a family of enzymes that unwind double-stranded (ds) RNA in a nucleoside triphosphate (NTP)-dependent fashion and which are required in all aspects of cellular RNA metabolism and processing. The hepatitis C virus (HCV) non-structural 3 (NS3) protein possesses a serine protease activity in the N-terminal one-third, whereas RNA-stimulated NTPase and helicase activities reside in the C-terminal portion of the 631 amino acid residue bifunctional enzyme. The HCV NS3 RNA helicase is of key importance in the life cycle of HCV, which makes it a target for the development of therapeutics. However, neither the precise mechanism nor the substrate structure has been defined for this enzyme. For nuclear magnetic resonance (NMR)-based drug discovery methods and for mechanistic studies we engineered, prepared and characterized various truncated constructs of the 451-residue HCV NS3 RNA helicase. Our goal was to produce smaller fragments of the enzyme, which would be amenable to solution NMR techniques while retaining their native NTP and/or nucleic acid binding sites. Solution conditions were optimized to obtain high-quality heteronuclear NMR spectra of nitrogen-15 isotope-labeled constructs, which are typical of well-folded monomeric proteins. Moreover, NMR binding studies and functional data directly support the correct folding of these fragments.
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Affiliation(s)
- J J Gesell
- These two authors contributed equally to this work. Department of Structural Chemistry, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
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McCoy MA, Senior MM, Gesell JJ, Ramanathan L, Wyss DF. Solution structure and dynamics of the single-chain hepatitis C virus NS3 protease NS4A cofactor complex. J Mol Biol 2001; 305:1099-110. [PMID: 11162117 DOI: 10.1006/jmbi.2000.4365] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [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: 11/22/2022]
Abstract
The backbone assignments, secondary structure, topology, and dynamics of the single-chain hepatitis C virus NS3 protease NS4A cofactor complex have been determined by NMR spectroscopy. Residues I34 to S181 of NS3 and the central three residues of the NS4A cofactor were assigned and the secondary structure was verified for these residues. In several X-ray structures of NS4A-bound NS3 protease, residues 1 to 28 are stabilized by crystal packing, which allows for the formation of the A0 strand and alpha0 helix. In solution, these N-terminal residues are largely unassigned and no evidence of a well-structured A0 strand or alpha0 helix was detected. NOEs between residues in the E1-F1 loop (containing D81) and the alpha1 helix (containing H57) together with the detection of a D81-H57 hydrogen bond indicate that in solution the catalytic triad (D81, H57, S139) of the protease is better ordered in the presence of the NS4A cofactor. This is consistent with the earlier crystallographic results and may explain the observed increase in catalytic activity of the enzyme due to NS4A binding. A model-free analysis of our relaxation data indicates substantial exchange rates for residues V51-D81, which comprise the upper part of the N-terminal beta-barrel. A comparison of chemical-shift differences between NS3 protease and the NS3 protease-NS4A complex shows extensive chemical-shift changes for residues V51-D81 indicating that non-local structural changes occur upon NS4A binding to the NS3 protease that are propagated well beyond the protease-cofactor interaction site. This is consistent with crystallographic data that reveal large structural rearrangements of the strand and loop regions formed by residues V51-D81 as a result of NS4A binding. The coincidence of large exchange rates for the NS3 protease-NS4A complex with chemical-shift differences due to NS4A binding suggests that residues V51-D81 of the NS3 protease NS4A complex are in slow exchange with a NS4A-free conformation of NS3 protease.
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Affiliation(s)
- M A McCoy
- Structural Chemistry Department, Schering Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
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