1
|
Sanders BC, Pokhrel S, Labbe AD, Mathews II, Cooper CJ, Davidson RB, Phillips G, Weiss KL, Zhang Q, O'Neill H, Kaur M, Schmidt JG, Reichard W, Surendranathan S, Parvathareddy J, Phillips L, Rainville C, Sterner DE, Kumaran D, Andi B, Babnigg G, Moriarty NW, Adams PD, Joachimiak A, Hurst BL, Kumar S, Butt TR, Jonsson CB, Ferrins L, Wakatsuki S, Galanie S, Head MS, Parks JM. Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Nat Commun 2023; 14:1733. [PMID: 36977673 PMCID: PMC10044120 DOI: 10.1038/s41467-023-37254-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we design a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibits PLpro with kinact/KI = 9,600 M-1 s-1, achieves sub-μM EC50 values against three SARS-CoV-2 variants in mammalian cell lines, and does not inhibit a panel of human deubiquitinases (DUBs) at >30 μM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validates our design strategy and establishes the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.
Collapse
Affiliation(s)
- Brian C Sanders
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Suman Pokhrel
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Biological Sciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Audrey D Labbe
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Hugh O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Manat Kaur
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jurgen G Schmidt
- B-11 Bioenergy and Biome Sciences, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Walter Reichard
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Surekha Surendranathan
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Lexi Phillips
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | | | | | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Babak Andi
- Center for BioMolecular Structure, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Gyorgy Babnigg
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Nigel W Moriarty
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paul D Adams
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Brett L Hurst
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | | | | | - Colleen B Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Lori Ferrins
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Soichi Wakatsuki
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Stephanie Galanie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Process Research and Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Martha S Head
- Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Computational and Data Sciences, Center for Research Acceleration by Digital Innovation, Amgen, Inc., Thosand Oaks, CA, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| |
Collapse
|
2
|
Joshi RP, Schultz KJ, Wilson JW, Kruel A, Varikoti RA, Kombala CJ, Kneller DW, Galanie S, Phillips G, Zhang Q, Coates L, Parvathareddy J, Surendranathan S, Kong Y, Clyde A, Ramanathan A, Jonsson CB, Brandvold KR, Zhou M, Head MS, Kovalevsky A, Kumar N. AI-Accelerated Design of Targeted Covalent Inhibitors for SARS-CoV-2. J Chem Inf Model 2023; 63:1438-1453. [PMID: 36808989 PMCID: PMC9969887 DOI: 10.1021/acs.jcim.2c01377] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/23/2023]
Abstract
Direct-acting antivirals for the treatment of the COVID-19 pandemic caused by the SARS-CoV-2 virus are needed to complement vaccination efforts. Given the ongoing emergence of new variants, automated experimentation, and active learning based fast workflows for antiviral lead discovery remain critical to our ability to address the pandemic's evolution in a timely manner. While several such pipelines have been introduced to discover candidates with noncovalent interactions with the main protease (Mpro), here we developed a closed-loop artificial intelligence pipeline to design electrophilic warhead-based covalent candidates. This work introduces a deep learning-assisted automated computational workflow to introduce linkers and an electrophilic "warhead" to design covalent candidates and incorporates cutting-edge experimental techniques for validation. Using this process, promising candidates in the library were screened, and several potential hits were identified and tested experimentally using native mass spectrometry and fluorescence resonance energy transfer (FRET)-based screening assays. We identified four chloroacetamide-based covalent inhibitors of Mpro with micromolar affinities (KI of 5.27 μM) using our pipeline. Experimentally resolved binding modes for each compound were determined using room-temperature X-ray crystallography, which is consistent with the predicted poses. The induced conformational changes based on molecular dynamics simulations further suggest that the dynamics may be an important factor to further improve selectivity, thereby effectively lowering KI and reducing toxicity. These results demonstrate the utility of our modular and data-driven approach for potent and selective covalent inhibitor discovery and provide a platform to apply it to other emerging targets.
Collapse
Affiliation(s)
- Rajendra P. Joshi
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Katherine J. Schultz
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Jesse William Wilson
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Agustin Kruel
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Rohith Anand Varikoti
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
| | - Chathuri J. Kombala
- Elson S. Floyd College of Medicine, Department of
Nutrition and Exercise Physiology, Washington State University,
Spokane, Washington 99202, United States
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Stephanie Galanie
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
- Department of Process Research and Development,
Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, New
Jersey 07065, United States
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Leighton Coates
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Second Target Station, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Surekha Surendranathan
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Ying Kong
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
| | - Austin Clyde
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
| | - Arvind Ramanathan
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
| | - Colleen B. Jonsson
- Regional Biocontainment Laboratory, The
University of Tennessee Health Science Center, Memphis, Tennessee 38105,
United States
- Institute for the Study of Host-Pathogen Systems,
University of Tennessee Health Science Center, Memphis,
Tennessee 38103, United States
- Department of Microbiology, Immunology and
Biochemistry, University of Tennessee Health Science Center,
Memphis, Tennessee 38103, United States
| | - Kristoffer R. Brandvold
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- Elson S. Floyd College of Medicine, Department of
Nutrition and Exercise Physiology, Washington State University,
Spokane, Washington 99202, United States
| | - Mowei Zhou
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Martha S. Head
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
- Joint Institute for Biological Sciences,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,
United States
- Center for Research Acceleration by Digital
Innovation, Amgen Research, Thousand Oaks, California 91320,
United States
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| | - Neeraj Kumar
- Earth and Biological Sciences Directorate,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology Laboratory,
US Department of Energy, Washington, District of Columbia
20585, United States
| |
Collapse
|
3
|
Andi B, Kumaran D, Kreitler DF, Soares AS, Keereetaweep J, Jakoncic J, Lazo EO, Shi W, Fuchs MR, Sweet RM, Shanklin J, Adams PD, Schmidt JG, Head MS, McSweeney S. Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease. Sci Rep 2022; 12:12197. [PMID: 35842458 PMCID: PMC9287821 DOI: 10.1038/s41598-022-15930-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 07/01/2022] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), threatens global public health. The world needs rapid development of new antivirals and vaccines to control the current pandemic and to control the spread of the variants. Among the proteins synthesized by the SARS-CoV-2 genome, main protease (Mpro also known as 3CLpro) is a primary drug target, due to its essential role in maturation of the viral polyproteins. In this study, we provide crystallographic evidence, along with some binding assay data, that three clinically approved anti hepatitis C virus drugs and two other drug-like compounds covalently bind to the Mpro Cys145 catalytic residue in the active site. Also, molecular docking studies can provide additional insight for the design of new antiviral inhibitors for SARS-CoV-2 using these drugs as lead compounds. One might consider derivatives of these lead compounds with higher affinity to the Mpro as potential COVID-19 therapeutics for further testing and possibly clinical trials.
Collapse
Affiliation(s)
- Babak Andi
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA.
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA.
| | - Dale F Kreitler
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Alexei S Soares
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | | | - Jean Jakoncic
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Edwin O Lazo
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Wuxian Shi
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Martin R Fuchs
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Robert M Sweet
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA
| | - Jurgen G Schmidt
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA
| | - Martha S Head
- Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA
| | - Sean McSweeney
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA.
| |
Collapse
|
4
|
Clyde A, Galanie S, Kneller DW, Ma H, Babuji Y, Blaiszik B, Brace A, Brettin T, Chard K, Chard R, Coates L, Foster I, Hauner D, Kertesz V, Kumar N, Lee H, Li Z, Merzky A, Schmidt JG, Tan L, Titov M, Trifan A, Turilli M, Van Dam H, Chennubhotla SC, Jha S, Kovalevsky A, Ramanathan A, Head MS, Stevens R. High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. J Chem Inf Model 2022; 62:116-128. [PMID: 34793155 PMCID: PMC8610012 DOI: 10.1021/acs.jcim.1c00851] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Indexed: 12/27/2022]
Abstract
Despite the recent availability of vaccines against the acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the search for inhibitory therapeutic agents has assumed importance especially in the context of emerging new viral variants. In this paper, we describe the discovery of a novel noncovalent small-molecule inhibitor, MCULE-5948770040, that binds to and inhibits the SARS-Cov-2 main protease (Mpro) by employing a scalable high-throughput virtual screening (HTVS) framework and a targeted compound library of over 6.5 million molecules that could be readily ordered and purchased. Our HTVS framework leverages the U.S. supercomputing infrastructure achieving nearly 91% resource utilization and nearly 126 million docking calculations per hour. Downstream biochemical assays validate this Mpro inhibitor with an inhibition constant (Ki) of 2.9 μM (95% CI 2.2, 4.0). Furthermore, using room-temperature X-ray crystallography, we show that MCULE-5948770040 binds to a cleft in the primary binding site of Mpro forming stable hydrogen bond and hydrophobic interactions. We then used multiple μs-time scale molecular dynamics (MD) simulations and machine learning (ML) techniques to elucidate how the bound ligand alters the conformational states accessed by Mpro, involving motions both proximal and distal to the binding site. Together, our results demonstrate how MCULE-5948770040 inhibits Mpro and offers a springboard for further therapeutic design.
Collapse
Affiliation(s)
- Austin Clyde
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Stephanie Galanie
- Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Heng Ma
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Yadu Babuji
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ben Blaiszik
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Alexander Brace
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Thomas Brettin
- Computing Environment and Life Sciences Directorate,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Kyle Chard
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ryan Chard
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ian Foster
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Darin Hauner
- Computational Biology Group, Biological Science Division,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Vlimos Kertesz
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Neeraj Kumar
- Computational Biology Group, Biological Science Division,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Hyungro Lee
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Zhuozhao Li
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Andre Merzky
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Jurgen G. Schmidt
- Bioscience Division, Los Alamos National
Laboratory, Los Alamos, New Mexico 87545, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Li Tan
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Mikhail Titov
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Anda Trifan
- University of Illinois at
Urbana-Champaign, Champaign, Illinois 61820, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Matteo Turilli
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Hubertus Van Dam
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Srinivas C. Chennubhotla
- Department of Computational and Systems
Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Shantenu Jha
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Andrey Kovalevsky
- Second Target Station, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Arvind Ramanathan
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Martha S. Head
- Joint Institute for Biological Sciences,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Rick Stevens
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- Computing Environment and Life Sciences Directorate,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| |
Collapse
|
5
|
Kneller DW, Li H, Galanie S, Phillips G, Labbé A, Weiss KL, Zhang Q, Arnould MA, Clyde A, Ma H, Ramanathan A, Jonsson CB, Head MS, Coates L, Louis JM, Bonnesen PV, Kovalevsky A. Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease. J Med Chem 2021; 64:17366-17383. [PMID: 34705466 PMCID: PMC8565456 DOI: 10.1021/acs.jmedchem.1c01475] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 02/08/2023]
Abstract
Creating small-molecule antivirals specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins is crucial to battle coronavirus disease 2019 (COVID-19). SARS-CoV-2 main protease (Mpro) is an established drug target for the design of protease inhibitors. We performed a structure-activity relationship (SAR) study of noncovalent compounds that bind in the enzyme's substrate-binding subsites S1 and S2, revealing structural, electronic, and electrostatic determinants of these sites. The study was guided by the X-ray/neutron structure of Mpro complexed with Mcule-5948770040 (compound 1), in which protonation states were directly visualized. Virtual reality-assisted structure analysis and small-molecule building were employed to generate analogues of 1. In vitro enzyme inhibition assays and room-temperature X-ray structures demonstrated the effect of chemical modifications on Mpro inhibition, showing that (1) maintaining correct geometry of an inhibitor's P1 group is essential to preserve the hydrogen bond with the protonated His163; (2) a positively charged linker is preferred; and (3) subsite S2 prefers nonbulky modestly electronegative groups.
Collapse
Affiliation(s)
- Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Hui Li
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stephanie Galanie
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Audrey Labbé
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| | - Mark A. Arnould
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Austin Clyde
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Department of Computer Science, University of Chicago, Chicago, IL 60615, USA
| | - Heng Ma
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Arvind Ramanathan
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60615
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Martha S. Head
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Leighton Coates
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA
| | - Peter V. Bonnesen
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, 20585, USA
| |
Collapse
|
6
|
Lobera M, Madauss KP, Pohlhaus DT, Wright QG, Trocha M, Schmidt DR, Baloglu E, Trump RP, Head MS, Hofmann GA, Murray-Thompson M, Schwartz B, Chakravorty S, Wu Z, Mander PK, Kruidenier L, Reid RA, Burkhart W, Turunen BJ, Rong JX, Wagner C, Moyer MB, Wells C, Hong X, Moore JT, Williams JD, Soler D, Ghosh S, Nolan MA. Selective class IIa histone deacetylase inhibition via a nonchelating zinc-binding group. Nat Chem Biol 2013; 9:319-25. [PMID: 23524983 DOI: 10.1038/nchembio.1223] [Citation(s) in RCA: 247] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 02/15/2013] [Indexed: 12/21/2022]
Abstract
In contrast to studies on class I histone deacetylase (HDAC) inhibitors, the elucidation of the molecular mechanisms and therapeutic potential of class IIa HDACs (HDAC4, HDAC5, HDAC7 and HDAC9) is impaired by the lack of potent and selective chemical probes. Here we report the discovery of inhibitors that fill this void with an unprecedented metal-binding group, trifluoromethyloxadiazole (TFMO), which circumvents the selectivity and pharmacologic liabilities of hydroxamates. We confirm direct metal binding of the TFMO through crystallographic approaches and use chemoproteomics to demonstrate the superior selectivity of the TFMO series relative to a hydroxamate-substituted analog. We further apply these tool compounds to reveal gene regulation dependent on the catalytic active site of class IIa HDACs. The discovery of these inhibitors challenges the design process for targeting metalloenzymes through a chelating metal-binding group and suggests therapeutic potential for class IIa HDAC enzyme blockers distinct in mechanism and application compared to current HDAC inhibitors.
Collapse
|
7
|
Green DVS, Leach AR, Head MS. Computer-aided molecular design under the SWOTlight. J Comput Aided Mol Des 2011; 26:51-6. [PMID: 22170256 DOI: 10.1007/s10822-011-9514-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 12/02/2011] [Indexed: 12/01/2022]
Affiliation(s)
- Darren V S Green
- GlaxoSmithKline Medicines Research Centre, Stevenage, Hertfordshire, UK.
| | | | | |
Collapse
|
8
|
Abstract
It is difficult to properly validate algorithms that dock a small molecule ligand into its protein receptor using data from the public domain: the predictions are not blind because the correct binding mode is already known, and public test cases may not be representative of compounds of interest such as drug leads. Here, we use private data from a real drug discovery program to carry out a blind evaluation of the RosettaLigand docking methodology and find that its performance is on average comparable with that of the best commercially available current small molecule docking programs. The strength of RosettaLigand is the use of the Rosetta sampling methodology to simultaneously optimize protein sidechain, protein backbone and ligand degrees of freedom; the extensive benchmark test described here identifies shortcomings in other aspects of the protocol and suggests clear routes to improving the method.
Collapse
Affiliation(s)
- Ian W Davis
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350, USA
| | | | | | | |
Collapse
|
9
|
Affiliation(s)
- Shashidhar N. Rao
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, Accelrys Inc., 9685 Scranton Road, San Diego, California 92121, and Chemistry Department, Bryn Mawr College, 101 North Merion Avenue, Bryn Mawr, Pennsylvania 19010
| | - Martha S. Head
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, Accelrys Inc., 9685 Scranton Road, San Diego, California 92121, and Chemistry Department, Bryn Mawr College, 101 North Merion Avenue, Bryn Mawr, Pennsylvania 19010
| | - Amit Kulkarni
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, Accelrys Inc., 9685 Scranton Road, San Diego, California 92121, and Chemistry Department, Bryn Mawr College, 101 North Merion Avenue, Bryn Mawr, Pennsylvania 19010
| | - Judith M. LaLonde
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, Accelrys Inc., 9685 Scranton Road, San Diego, California 92121, and Chemistry Department, Bryn Mawr College, 101 North Merion Avenue, Bryn Mawr, Pennsylvania 19010
| |
Collapse
|
10
|
Zhao B, Lehr R, Smallwood AM, Ho TF, Maley K, Randall T, Head MS, Koretke KK, Schnackenberg CG. Crystal structure of the kinase domain of serum and glucocorticoid-regulated kinase 1 in complex with AMP PNP. Protein Sci 2007; 16:2761-9. [PMID: 17965184 DOI: 10.1110/ps.073161707] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Serum and glucocorticoid-regulated kinase 1 (SGK1) is a serine/threonine protein kinase of the AGC family which participates in the control of epithelial ion transport and is implicated in proliferation and apoptosis. We report here the 1.9 A crystal structure of the catalytic domain of inactive human SGK1 in complex with AMP-PNP. SGK1 exists as a dimer formed by two intermolecular disulfide bonds between Cys258 in the activation loop and Cys193. Although most of the SGK1 structure closely resembles the common protein kinase fold, the structure around the active site is unique when compared to most protein kinases. The alphaC helix is not present in this inactive form of SGK1 crystal structure; instead, the segment corresponding to the C helix forms a beta-strand that is stabilized by the N-terminal segment of the activation loop through a short antiparallel beta-sheet. Since the differences from other kinases occur around the ATP binding site, this structure can provide valuable insight into the design of selective and highly potent ATP-competitive inhibitors of SGK1 kinase.
Collapse
Affiliation(s)
- Baoguang Zhao
- Department of Computational and Structural Chemistry, GlaxoSmithKline, King of Prussia, Pennsylvania 19406, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Stavenger RA, Cui H, Dowdell SE, Franz RG, Gaitanopoulos DE, Goodman KB, Hilfiker MA, Ivy RL, Leber JD, Marino JP, Oh HJ, Viet AQ, Xu W, Ye G, Zhang D, Zhao Y, Jolivette LJ, Head MS, Semus SF, Elkins PA, Kirkpatrick RB, Dul E, Khandekar SS, Yi T, Jung DK, Wright LL, Smith GK, Behm DJ, Doe CP, Bentley R, Chen ZX, Hu E, Lee D. Discovery of Aminofurazan-azabenzimidazoles as Inhibitors of Rho-Kinase with High Kinase Selectivity and Antihypertensive Activity. J Med Chem 2006; 50:2-5. [PMID: 17201404 DOI: 10.1021/jm060873p] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [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: 11/28/2022]
Abstract
The discovery, proposed binding mode, and optimization of a novel class of Rho-kinase inhibitors are presented. Appropriate substitution on the 6-position of the azabenzimidazole core provided subnanomolar enzyme potency in vitro while dramatically improving selectivity over a panel of other kinases. Pharmacokinetic data was obtained for the most potent and selective examples and one (6n) has been shown to lower blood pressure in a rat model of hypertension.
Collapse
Affiliation(s)
- Robert A Stavenger
- Department of Medicinal Chemistry, GlaxoSmithKline, King of Prussia, Pennsylvania 19406, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head MS. A critical assessment of docking programs and scoring functions. J Med Chem 2006; 49:5912-31. [PMID: 17004707 DOI: 10.1021/jm050362n] [Citation(s) in RCA: 1163] [Impact Index Per Article: 64.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Docking is a computational technique that samples conformations of small molecules in protein binding sites; scoring functions are used to assess which of these conformations best complements the protein binding site. An evaluation of 10 docking programs and 37 scoring functions was conducted against eight proteins of seven protein types for three tasks: binding mode prediction, virtual screening for lead identification, and rank-ordering by affinity for lead optimization. All of the docking programs were able to generate ligand conformations similar to crystallographically determined protein/ligand complex structures for at least one of the targets. However, scoring functions were less successful at distinguishing the crystallographic conformation from the set of docked poses. Docking programs identified active compounds from a pharmaceutically relevant pool of decoy compounds; however, no single program performed well for all of the targets. For prediction of compound affinity, none of the docking programs or scoring functions made a useful prediction of ligand binding affinity.
Collapse
Affiliation(s)
- Gregory L Warren
- GlaxoSmithKline Pharmaceuticals, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Yamashita DS, Marquis RW, Xie R, Nidamarthy SD, Oh HJ, Jeong JU, Erhard KF, Ward KW, Roethke TJ, Smith BR, Cheng HY, Geng X, Lin F, Offen PH, Wang B, Nevins N, Head MS, Haltiwanger RC, Narducci Sarjeant AA, Liable-Sands LM, Zhao B, Smith WW, Janson CA, Gao E, Tomaszek T, McQueney M, James IE, Gress CJ, Zembryki DL, Lark MW, Veber DF. Structure activity relationships of 5-, 6-, and 7-methyl-substituted azepan-3-one cathepsin K inhibitors. J Med Chem 2006; 49:1597-612. [PMID: 16509577 DOI: 10.1021/jm050915u] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [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: 11/29/2022]
Abstract
The syntheses, in vitro characterizations, and rat and monkey in vivo pharmacokinetic profiles of a series of 5-, 6-, and 7-methyl-substituted azepanone-based cathepsin K inhibitors are described. Depending on the particular regiochemical substitution and stereochemical configuration, methyl-substituted azepanones were identified that had widely varied cathepsin K inhibitory potency as well as pharmacokinetic properties compared to the 4S-parent azepanone analogue, 1 (human cathepsin K, K(i,app) = 0.16 nM, rat oral bioavailability = 42%, rat in vivo clearance = 49.2 mL/min/kg). Of particular note, the 4S-7-cis-methylazepanone analogue, 10, had a K(i,app) = 0.041 nM vs human cathepsin K and 89% oral bioavailability and an in vivo clearance rate of 19.5 mL/min/kg in the rat. Hypotheses that rationalize some of the observed characteristics of these closely related analogues have been made using X-ray crystallography and conformational analysis. These examples demonstrate the potential for modulation of pharmacological properties of cathepsin inhibitors by substituting the azepanone core. The high potency for inhibition of cathepsin K coupled with the favorable rat and monkey pharmacokinetic characteristics of compound 10, also known as SB-462795 or relacatib, has made it the subject of considerable in vivo evaluation for safety and efficacy as an inhibitor of excessive bone resorption in rat, monkey, and human studies, which will be reported elsewhere.
Collapse
Affiliation(s)
- Dennis S Yamashita
- Department of Medicinal Chemistry, GlaxoSmithKline, 1250 S. Collegeville Rd, Collegeville, Pennsylvania 19426, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Marquis RW, James I, Zeng J, Trout REL, Thompson S, Rahman A, Yamashita DS, Xie R, Ru Y, Gress CJ, Blake S, Lark MA, Hwang SM, Tomaszek T, Offen P, Head MS, Cummings MD, Veber DF. Azepanone-Based Inhibitors of Human Cathepsin L. J Med Chem 2005; 48:6870-8. [PMID: 16250645 DOI: 10.1021/jm0502079] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [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: 11/30/2022]
Abstract
The extension of a previously reported cathepsin K azepanone-based inhibitor template to the design and synthesis of potent and selective inhibitors of the homologous cysteine protease cathepsin L is detailed. Structure-activity studies examining the effect of inhibitor selectivity as a function of the P3 and P2 binding elements of the potent cathepsin K inhibitor 1 revealed that incorporation of either a P3 quinoline-8-carboxamide or a naphthylene-1-carboxamide led to increased selectivity for cathepsin L over cathepsin K. Substitution of the P2 leucine of 1 with either a phenylalanine or a beta-naphthylalanine also resulted in an increased selectivity for cathepsin L over cathepsin K. Molecular modeling studies with the inhibitors docked within the active sites of both cathepsins L and K have rationalized the observed selectivities. Optimization of cathepsin L binding by the combination of the P3 naphthylene-1-carboxamide with the P2 beta-naphthylalanine provided 15, which is a potent, selective, and competitive inhibitor of human cathepsin L with a K(i) = 0.43 nM.
Collapse
Affiliation(s)
- Robert W Marquis
- Department of Medicinal Chemistry, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Seefeld MA, Miller WH, Newlander KA, Burgess WJ, DeWolf WE, Elkins PA, Head MS, Jakas DR, Janson CA, Keller PM, Manley PJ, Moore TD, Payne DJ, Pearson S, Polizzi BJ, Qiu X, Rittenhouse SF, Uzinskas IN, Wallis NG, Huffman WF. Indole naphthyridinones as inhibitors of bacterial enoyl-ACP reductases FabI and FabK. J Med Chem 2003; 46:1627-35. [PMID: 12699381 DOI: 10.1021/jm0204035] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial enoyl-ACP reductase (FabI) is responsible for catalyzing the final step of bacterial fatty acid biosynthesis and is an attractive target for the development of novel antibacterial agents. Previously we reported the development of FabI inhibitor 4 with narrow spectrum antimicrobial activity and in vivo efficacy against Staphylococcus aureus via intraperitoneal (ip) administration. Through iterative medicinal chemistry aided by X-ray crystal structure analysis, a new series of inhibitors has been developed with greatly increased potency against FabI-containing organisms. Several of these new inhibitors have potent antibacterial activity against multidrug resistant strains of S. aureus, and compound 30 demonstrates exceptional oral (po) in vivo efficacy in a S. aureus infection model in rats. While optimizing FabI inhibitory activity, compounds 29 and 30 were identified as having low micromolar FabK inhibitory activity, thereby increasing the antimicrobial spectrum of these compounds to include the FabK-containing pathogens Streptococcus pneumoniae and Enterococcus faecalis. The results described herein support the hypothesis that bacterial enoyl-ACP reductases are valid targets for antibacterial agents.
Collapse
Affiliation(s)
- Mark A Seefeld
- GlaxoSmithKline Pharmaceuticals, 1250 South Collegeville Road, P.O. Box 5089, Collegeville, Pennsylvania 19426, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Daines RA, Pendrak I, Sham K, Van Aller GS, Konstantinidis AK, Lonsdale JT, Janson CA, Qiu X, Brandt M, Khandekar SS, Silverman C, Head MS. First X-ray cocrystal structure of a bacterial FabH condensing enzyme and a small molecule inhibitor achieved using rational design and homology modeling. J Med Chem 2003; 46:5-8. [PMID: 12502353 DOI: 10.1021/jm025571b] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [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 first cocrystal structure of a bacterial FabH condensing enzyme and a small molecule inhibitor is reported. The inhibitor was obtained by rational modification of a high throughput screening lead with the aid of a S. pneumoniae FabH homology model. This homology model was used to design analogues that would have both high affinity for the enzyme and appropriate aqueous solubility to facilitate cocrystallization studies.
Collapse
Affiliation(s)
- Robert A Daines
- Department of Medicinal Chemistry, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Fan F, Yan K, Wallis NG, Reed S, Moore TD, Rittenhouse SF, DeWolf WE, Huang J, McDevitt D, Miller WH, Seefeld MA, Newlander KA, Jakas DR, Head MS, Payne DJ. Defining and combating the mechanisms of triclosan resistance in clinical isolates of Staphylococcus aureus. Antimicrob Agents Chemother 2002; 46:3343-7. [PMID: 12384334 PMCID: PMC128739 DOI: 10.1128/aac.46.11.3343-3347.2002] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [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: 11/20/2022] Open
Abstract
The MICs of triclosan for 31 clinical isolates of Staphylococcus aureus were 0.016 micro g/ml (24 strains), 1 to 2 micro g/ml (6 strains), and 0.25 micro g/ml (1 strain). All the strains for which triclosan MICs were elevated (>0.016 micro g/ml) showed three- to fivefold increases in their levels of enoyl-acyl carrier protein (ACP) reductase (FabI) production. Furthermore, strains for which triclosan MICs were 1 to 2 micro g/ml overexpressed FabI with an F204C alteration. Binding studies with radiolabeled NAD(+) demonstrated that this change prevents the formation of the stable triclosan-NAD(+)-FabI complex, and both this alteration and its overexpression contributed to achieving MICs of 1 to 2 micro g/ml for these strains. Three novel, potent inhibitors of FabI (50% inhibitory concentrations, < or =64 nM) demonstrated up to 1,000-fold better activity than triclosan against the strains for which triclosan MICs were elevated. None of the compounds tested from this series formed a stable complex with NAD(+)-FabI. Consequently, although the overexpression of wild-type FabI gave rise to an increase in the MICs, as expected, overexpression of FabI with an F204C alteration did not cause an additional increase in resistance. Therefore, this work identifies the mechanisms of triclosan resistance in S. aureus, and we present three compounds from a novel chemical series of FabI inhibitors which have excellent activities against both triclosan-resistant and -sensitive clinical isolates of S. aureus.
Collapse
Affiliation(s)
- Frank Fan
- Microbial, Musculoskeletal and Proliferative Diseases CEDD. Computational and Structural Sciences, GlaxoSmithKline Pharmaceuticals, Collegeville, Pennsylvania 19426, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Payne DJ, Miller WH, Berry V, Brosky J, Burgess WJ, Chen E, DeWolf WE, Fosberry AP, Greenwood R, Head MS, Heerding DA, Janson CA, Jaworski DD, Keller PM, Manley PJ, Moore TD, Newlander KA, Pearson S, Polizzi BJ, Qiu X, Rittenhouse SF, Slater-Radosti C, Salyers KL, Seefeld MA, Smyth MG, Takata DT, Uzinskas IN, Vaidya K, Wallis NG, Winram SB, Yuan CCK, Huffman WF. Discovery of a novel and potent class of FabI-directed antibacterial agents. Antimicrob Agents Chemother 2002; 46:3118-24. [PMID: 12234833 PMCID: PMC128775 DOI: 10.1128/aac.46.10.3118-3124.2002] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.0] [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: 11/20/2022] Open
Abstract
Bacterial enoyl-acyl carrier protein (ACP) reductase (FabI) catalyzes the final step in each elongation cycle of bacterial fatty acid biosynthesis and is an attractive target for the development of new antibacterial agents. High-throughput screening of the Staphylococcus aureus FabI enzyme identified a novel, weak inhibitor with no detectable antibacterial activity against S. aureus. Iterative medicinal chemistry and X-ray crystal structure-based design led to the identification of compound 4 [(E)-N-methyl-N-(2-methyl-1H-indol-3-ylmethyl)-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)acrylamide], which is 350-fold more potent than the original lead compound obtained by high-throughput screening in the FabI inhibition assay. Compound 4 has exquisite antistaphylococci activity, achieving MICs at which 90% of isolates are inhibited more than 500 times lower than those of nine currently available antibiotics against a panel of multidrug-resistant strains of S. aureus and Staphylococcus epidermidis. Furthermore, compound 4 exhibits excellent in vivo efficacy in an S. aureus infection model in rats. Biochemical and genetic approaches have confirmed that the mode of antibacterial action of compound 4 and related compounds is via inhibition of FabI. Compound 4 also exhibits weak FabK inhibitory activity, which may explain its antibacterial activity against Streptococcus pneumoniae and Enterococcus faecalis, which depend on FabK and both FabK and FabI, respectively, for their enoyl-ACP reductase function. These results show that compound 4 is representative of a new, totally synthetic series of antibacterial agents that has the potential to provide novel alternatives for the treatment of S. aureus infections that are resistant to our present armory of antibiotics.
Collapse
Affiliation(s)
- David J Payne
- Microbial, Musculoskeletal and Proliferative Diseases Center of Excellence in Drug Discovery, GlaxoSmithKline Pharmaceuticals, Collegeville, Pennsylvania 19426, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Miller WH, Seefeld MA, Newlander KA, Uzinskas IN, Burgess WJ, Heerding DA, Yuan CCK, Head MS, Payne DJ, Rittenhouse SF, Moore TD, Pearson SC, Berry V, DeWolf WE, Keller PM, Polizzi BJ, Qiu X, Janson CA, Huffman WF. Discovery of aminopyridine-based inhibitors of bacterial enoyl-ACP reductase (FabI). J Med Chem 2002; 45:3246-56. [PMID: 12109908 DOI: 10.1021/jm020050+] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial enoyl-ACP reductase (FabI) catalyzes the final step in each cycle of bacterial fatty acid biosynthesis and is an attractive target for the development of new antibacterial agents. Our efforts to identify potent, selective FabI inhibitors began with screening of the GlaxoSmithKline proprietary compound collection, which identified several small-molecule inhibitors of Staphylococcus aureus FabI. Through a combination of iterative medicinal chemistry and X-ray crystal structure based design, one of these leads was developed into the novel aminopyridine derivative 9, a low micromolar inhibitor of FabI from S. aureus (IC(50) = 2.4 microM) and Haemophilus influenzae (IC(50) = 4.2 microM). Compound 9 has good in vitro antibacterial activity against several organisms, including S. aureus (MIC = 0.5 microg/mL), and is effective in vivo in a S. aureus groin abscess infection model in rats. Through FabI overexpressor and macromolecular synthesis studies, the mode of action of 9 has been confirmed to be inhibition of fatty acid biosynthesis via inhibition of FabI. Taken together, these results support FabI as a valid antibacterial target and demonstrate the potential of small-molecule FabI inhibitors for the treatment of bacterial infections.
Collapse
Affiliation(s)
- William H Miller
- GlaxoSmithKline Pharmaceuticals, 1250 South Collegeville Road, P.O. Box 5089, Collegeville, PA 19426, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Head MS, Ryan MD, Lee D, Feng Y, Janson CA, Concha NO, Keller PM, deWolf WE. Structure-based combinatorial library design: discovery of non-peptidic inhibitors of caspases 3 and 8. J Comput Aided Mol Des 2001; 15:1105-17. [PMID: 12160093 DOI: 10.1023/a:1015976725743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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]
Abstract
Structure-based design of a combinatorial array was carried out in order to identify non-peptidic thiomethylketone inhibitors of caspases 3 and 8. Five compounds from the designed array were active against caspase 3, and two were active against caspase 8. A 2.5-A resolution co-crystal structure of caspase 3 and a thiomethylketone array member is reported. The structure-based design strategy has proved useful for identifying caspase inhibitors.
Collapse
Affiliation(s)
- M S Head
- Physical and Structural Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406, USA.
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Lee D, Long SA, Adams JL, Chan G, Vaidya KS, Francis TA, Kikly K, Winkler JD, Sung CM, Debouck C, Richardson S, Levy MA, DeWolf WE, Keller PM, Tomaszek T, Head MS, Ryan MD, Haltiwanger RC, Liang PH, Janson CA, McDevitt PJ, Johanson K, Concha NO, Chan W, Abdel-Meguid SS, Badger AM, Lark MW, Nadeau DP, Suva LJ, Gowen M, Nuttall ME. Potent and selective nonpeptide inhibitors of caspases 3 and 7 inhibit apoptosis and maintain cell functionality. J Biol Chem 2000; 275:16007-14. [PMID: 10821855 DOI: 10.1074/jbc.275.21.16007] [Citation(s) in RCA: 183] [Impact Index Per Article: 7.6] [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: 11/06/2022] Open
Abstract
Caspases have been strongly implicated to play an essential role in apoptosis. A critical question regarding the role(s) of these proteases is whether selective inhibition of an effector caspase(s) will prevent cell death. We have identified potent and selective non-peptide inhibitors of the effector caspases 3 and 7. The inhibition of apoptosis and maintenance of cell functionality with a caspase 3/7-selective inhibitor is demonstrated for the first time, and suggests that targeting these two caspases alone is sufficient for blocking apoptosis. Furthermore, an x-ray co-crystal structure of the complex between recombinant human caspase 3 and an isatin sulfonamide inhibitor has been solved to 2.8-A resolution. In contrast to previously reported peptide-based caspase inhibitors, the isatin sulfonamides derive their selectivity for caspases 3 and 7 by interacting primarily with the S(2) subsite, and do not bind in the caspase primary aspartic acid binding pocket (S(1)). These inhibitors blocked apoptosis in murine bone marrow neutrophils and human chondrocytes. Furthermore, in camptothecin-induced chondrocyte apoptosis, cell functionality as measured by type II collagen promoter activity is maintained, an activity considered essential for cartilage homeostasis. These data suggest that inhibiting chondrocyte cell death with a caspase 3/7-selective inhibitor may provide a novel therapeutic approach for the prevention and treatment of osteoarthritis, or other disease states characterized by excessive apoptosis.
Collapse
Affiliation(s)
- D Lee
- Department of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Abstract
A recently developed computational method, 'mining minima', is used to examine the hydrogen-bonding interactions of nucleic acid base-pairs and of the N-methylacetamide homodimer in chloroform. The mining minima algorithm aggressively samples molecular conformations, identifies the most important local minima, and computes their contributions to the overall free energy of the system. Here, the CHARMM 98 parameter set is used for the potential energy and the generalized Born/surface area solvent model is used to account for the influence of the solvent. Good agreement with experiment is obtained for the non-covalent binding affinities of a series of complexes. The computational approach used here is applicable to a range of molecular systems.
Collapse
Affiliation(s)
- R Luo
- Center for Advanced Research in Biotechnology, Rockville, MD 20850, USA
| | | | | | | |
Collapse
|
23
|
David L, Luo R, Head MS, Gilson MK. Computational Study of KNI-272, a Potent Inhibitor of HIV-1 Protease: On the Mechanism of Preorganization. J Phys Chem B 1999. [DOI: 10.1021/jp983675l] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Laurent David
- Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, Maryland 20850, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, and SmithKline Beecham Pharmaceuticals, UW 2950, 709 Swedeland Road, P.O. Box 1539, King of Prussia, Pennsylvania 19406-0939
| | - Ray Luo
- Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, Maryland 20850, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, and SmithKline Beecham Pharmaceuticals, UW 2950, 709 Swedeland Road, P.O. Box 1539, King of Prussia, Pennsylvania 19406-0939
| | - Martha S. Head
- Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, Maryland 20850, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, and SmithKline Beecham Pharmaceuticals, UW 2950, 709 Swedeland Road, P.O. Box 1539, King of Prussia, Pennsylvania 19406-0939
| | - Michael K. Gilson
- Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, Maryland 20850, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, and SmithKline Beecham Pharmaceuticals, UW 2950, 709 Swedeland Road, P.O. Box 1539, King of Prussia, Pennsylvania 19406-0939
| |
Collapse
|
24
|
Trylska J, Antosiewicz J, Geller M, Hodge CN, Klabe RM, Head MS, Gilson MK. Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease. Protein Sci 1999; 8:180-95. [PMID: 10210196 PMCID: PMC2144115 DOI: 10.1110/ps.8.1.180] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The aspartyl dyad of free HIV-1 protease has apparent pK(a)s of approximately 3 and approximately 6, but recent NMR studies indicate that the aspartyl dyad is fixed in the doubly protonated form over a wide pH range when cyclic urea inhibitors are bound, and in the monoprotonated form when the inhibitor KNI-272 is bound. We present computations and measurements related to these changes in protonation and to the thermodynamic linkage between protonation and inhibition. The Poisson-Boltzmann model of electrostatics is used to compute the apparent pK(a)s of the aspartyl dyad in the free enzyme and in complexes with four different inhibitors. The calculations are done with two parameter sets. One assigns epsilon = 4 to the solute interior and uses a detailed model of ionization; the other uses epsilon = 20 for the solute interior and a simplified representation of ionization. For the free enzyme, both parameter sets agree well with previously measured apparent pK(a)s of approximately 3 and approximately 6. However, the calculations with an internal dielectric constant of 4 reproduce the large pKa shifts upon binding of inhibitors, but the calculations with an internal dielectric constant of 20 do not. This observation has implications for the accurate calculation of pK(a)s in complex protein environments. Because binding of a cyclic urea inhibitor shifts the pK(a)s of the aspartyl dyad, changing the pH is expected to change its apparent binding affinity. However, we find experimentally that the affinity is independent of pH from 5.5 to 7.0. Possible explanations for this discrepancy are discussed.
Collapse
Affiliation(s)
- J Trylska
- Department of Biophysics, University of Warsaw, Poland.
| | | | | | | | | | | | | |
Collapse
|
25
|
Marquis RW, Yamashita DS, Ru Y, LoCastro SM, Oh HJ, Erhard KF, DesJarlais RL, Head MS, Smith WW, Zhao B, Janson CA, Abdel-Meguid SS, Tomaszek TA, Levy MA, Veber DF. Conformationally constrained 1,3-diamino ketones: a series of potent inhibitors of the cysteine protease cathepsin K. J Med Chem 1998; 41:3563-7. [PMID: 9733481 DOI: 10.1021/jm980295f] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- R W Marquis
- Departments of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Affiliation(s)
- Rui Luo
- Contribution from the Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850, Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, Maryland 20742, and National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Martha S. Head
- Contribution from the Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850, Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, Maryland 20742, and National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - John Moult
- Contribution from the Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850, Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, Maryland 20742, and National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Michael K. Gilson
- Contribution from the Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850, Department of Chemistry and Biochemistry, University of Maryland at College Park, College Park, Maryland 20742, and National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| |
Collapse
|
27
|
Affiliation(s)
- Martha S. Head
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850
| | - James A. Given
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850
| | - Michael K. Gilson
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850
| |
Collapse
|
28
|
Abstract
Models for predicting the binding affinities of molecules in solution are either very detailed, making them computationally intensive and hard to test, or very simple, and thus less informative than one might wish. A new class of models that focus on the predominant states of the binding molecules promise to capture the essential physics of binding at modest computational cost.
Collapse
Affiliation(s)
- M K Gilson
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850 USA.
| | | | | |
Collapse
|