1
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Chandramohan A, Josien H, Yuen TY, Duggal R, Spiegelberg D, Yan L, Juang YCA, Ge L, Aronica PG, Kaan HYK, Lim YH, Peier A, Sherborne B, Hochman J, Lin S, Biswas K, Nestor M, Verma CS, Lane DP, Sawyer TK, Garbaccio R, Henry B, Kannan S, Brown CJ, Johannes CW, Partridge AW. Design-rules for stapled peptides with in vivo activity and their application to Mdm2/X antagonists. Nat Commun 2024; 15:489. [PMID: 38216578 PMCID: PMC10786919 DOI: 10.1038/s41467-023-43346-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 04/01/2023] [Accepted: 11/06/2023] [Indexed: 01/14/2024] Open
Abstract
Although stapled α-helical peptides can address challenging targets, their advancement is impeded by poor understandings for making them cell permeable while avoiding off-target toxicities. By synthesizing >350 molecules, we present workflows for identifying stapled peptides against Mdm2(X) with in vivo activity and no off-target effects. Key insights include a clear correlation between lipophilicity and permeability, removal of positive charge to avoid off-target toxicities, judicious anionic residue placement to enhance solubility/behavior, optimization of C-terminal length/helicity to enhance potency, and optimization of staple type/number to avoid polypharmacology. Workflow application gives peptides with >292x improved cell proliferation potencies and no off-target cell proliferation effects ( > 3800x on-target index). Application of these 'design rules' to a distinct Mdm2(X) peptide series improves ( > 150x) cellular potencies and removes off-target toxicities. The outlined workflow should facilitate therapeutic impacts, especially for those targets such as Mdm2(X) that have hydrophobic interfaces and are targetable with a helical motif.
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Affiliation(s)
| | | | - Tsz Ying Yuen
- Institute of Sustainability for Chemicals, Energy and Environment, Agency for Science, Technology and Research (ASTAR), Singapore, 138665, Singapore
| | | | - Diana Spiegelberg
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Lin Yan
- Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | | | - Lan Ge
- Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | - Pietro G Aronica
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, 138671, Singapore
| | | | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment, Agency for Science, Technology and Research (ASTAR), Singapore, 138665, Singapore
| | | | | | | | | | | | - Marika Nestor
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, 138671, Singapore
| | - David P Lane
- Institute of Molecular and Cell Biology, Singapore, 138673, Singapore
| | | | | | - Brian Henry
- MSD International, Singapore, 138665, Singapore.
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, 138671, Singapore.
| | | | - Charles W Johannes
- Institute of Sustainability for Chemicals, Energy and Environment, Agency for Science, Technology and Research (ASTAR), Singapore, 138665, Singapore.
- Institute of Molecular and Cell Biology, Singapore, 138673, Singapore.
- EPOC Scientific LLC, Stoneham, MA, 02180, USA.
| | - Anthony W Partridge
- MSD International, Singapore, 138665, Singapore.
- Genentech, South San Francisco, CA, 94080, USA.
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2
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Peier A, Ge L, Boyer N, Frost J, Duggal R, Biswas K, Edmondson S, Hermes JD, Yan L, Zimprich C, Sadruddin A, Kristal Kaan HY, Chandramohan A, Brown CJ, Thean D, Lee XE, Yuen TY, Ferrer-Gago FJ, Johannes CW, Lane DP, Sherborne B, Corona C, Robers MB, Sawyer TK, Partridge AW. NanoClick: A High Throughput, Target-Agnostic Peptide Cell Permeability Assay. ACS Chem Biol 2021; 16:293-309. [PMID: 33539064 DOI: 10.1021/acschembio.0c00804] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Macrocyclic peptides open new opportunities to target intracellular protein-protein interactions (PPIs) that are often considered nondruggable by traditional small molecules. However, engineering sufficient membrane permeability into these molecules is a central challenge for identifying clinical candidates. Currently, there is a lack of high-throughput assays to assess peptide permeability, which limits our capacity to engineer this property into macrocyclic peptides for advancement through drug discovery pipelines. Accordingly, we developed a high throughput and target-agnostic cell permeability assay that measures the relative cumulative cytosolic exposure of a peptide in a concentration-dependent manner. The assay was named NanoClick as it combines in-cell Click chemistry with an intracellular NanoBRET signal. We validated the approach using known cell penetrating peptides and further demonstrated a correlation to cellular activity using a p53/MDM2 model system. With minimal change to the peptide sequence, NanoClick enables the ability to measure uptake of molecules that enter the cell via different mechanisms such as endocytosis, membrane translocation, or passive permeability. Overall, the NanoClick assay can serve as a screening tool to uncover predictive design rules to guide structure-activity-permeability relationships in the optimization of functionally active molecules.
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Affiliation(s)
- Andrea Peier
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Lan Ge
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Nicolas Boyer
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - John Frost
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Ruchia Duggal
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Kaustav Biswas
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Scott Edmondson
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - Lin Yan
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Chad Zimprich
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | | | | | - Christopher J. Brown
- Agency for Science, Technology and Research (A*STAR) Singapore 138665, Singapore
| | - Dawn Thean
- Agency for Science, Technology and Research (A*STAR) Singapore 138665, Singapore
| | - Xue Er Lee
- Agency for Science, Technology and Research (A*STAR) Singapore 138665, Singapore
| | - Tsz Ying Yuen
- Agency for Science, Technology and Research (A*STAR) Singapore 138665, Singapore
| | | | - Charles W. Johannes
- Agency for Science, Technology and Research (A*STAR) Singapore 138665, Singapore
| | - David P. Lane
- Agency for Science, Technology and Research (A*STAR) Singapore 138665, Singapore
| | - Brad Sherborne
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Cesear Corona
- Promega Biosciences Incorporated, San Luis Obispo, California 93401, United States
| | | | - Tomi K. Sawyer
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
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3
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Partridge AW, Kaan HYK, Juang YC, Sadruddin A, Lim S, Brown CJ, Ng S, Thean D, Ferrer F, Johannes C, Yuen TY, Kannan S, Aronica P, Tan YS, Pradhan MR, Verma CS, Hochman J, Chen S, Wan H, Ha S, Sherborne B, Lane DP, Sawyer TK. Incorporation of Putative Helix-Breaking Amino Acids in the Design of Novel Stapled Peptides: Exploring Biophysical and Cellular Permeability Properties. Molecules 2019; 24:E2292. [PMID: 31226791 PMCID: PMC6632053 DOI: 10.3390/molecules24122292] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [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: 05/22/2019] [Revised: 06/14/2019] [Accepted: 06/16/2019] [Indexed: 12/21/2022] Open
Abstract
Stapled α-helical peptides represent an emerging superclass of macrocyclic molecules with drug-like properties, including high-affinity target binding, protease resistance, and membrane permeability. As a model system for probing the chemical space available for optimizing these properties, we focused on dual Mdm2/MdmX antagonist stapled peptides related to the p53 N-terminus. Specifically, we first generated a library of ATSP-7041 (Chang et al., 2013) analogs iteratively modified by L-Ala and D-amino acids. Single L-Ala substitutions beyond the Mdm2/(X) binding interfacial residues (i.e., Phe3, Trp7, and Cba10) had minimal effects on target binding, α-helical content, and cellular activity. Similar binding affinities and cellular activities were noted at non-interfacial positions when the template residues were substituted with their d-amino acid counterparts, despite the fact that d-amino acid residues typically 'break' right-handed α-helices. d-amino acid substitutions at the interfacial residues Phe3 and Cba10 resulted in the expected decreases in binding affinity and cellular activity. Surprisingly, substitution at the remaining interfacial position with its d-amino acid equivalent (i.e., Trp7 to d-Trp7) was fully tolerated, both in terms of its binding affinity and cellular activity. An X-ray structure of the d-Trp7-modified peptide was determined and revealed that the indole side chain was able to interact optimally with its Mdm2 binding site by a slight global re-orientation of the stapled peptide. To further investigate the comparative effects of d-amino acid substitutions we used linear analogs of ATSP-7041, where we replaced the stapling amino acids by Aib (i.e., R84 to Aib4 and S511 to Aib11) to retain the helix-inducing properties of α-methylation. The resultant analog sequence Ac-Leu-Thr-Phe-Aib-Glu-Tyr-Trp-Gln-Leu-Cba-Aib-Ser-Ala-Ala-NH2 exhibited high-affinity target binding (Mdm2 Kd = 43 nM) and significant α-helicity in circular dichroism studies. Relative to this linear ATSP-7041 analog, several d-amino acid substitutions at Mdm2(X) non-binding residues (e.g., d-Glu5, d-Gln8, and d-Leu9) demonstrated decreased binding and α-helicity. Importantly, circular dichroism (CD) spectroscopy showed that although helicity was indeed disrupted by d-amino acids in linear versions of our template sequence, stapled molecules tolerated these residues well. Further studies on stapled peptides incorporating N-methylated amino acids, l-Pro, or Gly substitutions showed that despite some positional dependence, these helix-breaking residues were also generally tolerated in terms of secondary structure, binding affinity, and cellular activity. Overall, macrocyclization by hydrocarbon stapling appears to overcome the destabilization of α-helicity by helix breaking residues and, in the specific case of d-Trp7-modification, a highly potent ATSP-7041 analog (Mdm2 Kd = 30 nM; cellular EC50 = 600 nM) was identified. Our findings provide incentive for future studies to expand the chemical diversity of macrocyclic α-helical peptides (e.g., d-amino acid modifications) to explore their biophysical properties and cellular permeability. Indeed, using the library of 50 peptides generated in this study, a good correlation between cellular permeability and lipophilicity was observed.
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Affiliation(s)
- Anthony W Partridge
- MSD International, 8 Biomedical Grove, #04-01/05 Neuros Building, Singapore 138665, Singapore.
| | - Hung Yi Kristal Kaan
- MSD International, 8 Biomedical Grove, #04-01/05 Neuros Building, Singapore 138665, Singapore.
| | - Yu-Chi Juang
- MSD International, 8 Biomedical Grove, #04-01/05 Neuros Building, Singapore 138665, Singapore.
| | - Ahmad Sadruddin
- MSD International, 8 Biomedical Grove, #04-01/05 Neuros Building, Singapore 138665, Singapore.
| | - Shuhui Lim
- MSD International, 8 Biomedical Grove, #04-01/05 Neuros Building, Singapore 138665, Singapore.
| | - Christopher J Brown
- p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore.
| | - Simon Ng
- p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore.
| | - Dawn Thean
- p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore.
| | - Fernando Ferrer
- p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore.
| | - Charles Johannes
- Institute of Chemical and Engineering Sciences (ICES), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07, Neuros Building, Singapore 138665, Singapore.
| | - Tsz Ying Yuen
- Institute of Chemical and Engineering Sciences (ICES), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, #07, Neuros Building, Singapore 138665, Singapore.
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Pietro Aronica
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Yaw Sing Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Mohan R Pradhan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Chandra S Verma
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | | | | | - Hui Wan
- Merck & Co., Inc., Kenilworth, NJ 07033, USA.
| | - Sookhee Ha
- Merck & Co., Inc., Kenilworth, NJ 07033, USA.
| | | | - David P Lane
- p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore.
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4
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Garton M, Corbi-Verge C, Hu Y, Nim S, Tarasova N, Sherborne B, Kim PM. Rapid and accurate structure-based therapeutic peptide design using GPU accelerated thermodynamic integration. Proteins 2019; 87:236-244. [PMID: 30520126 DOI: 10.1002/prot.25644] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 06/19/2018] [Revised: 10/30/2018] [Accepted: 11/29/2018] [Indexed: 11/07/2022]
Abstract
Peptide-based therapeutics are an alternative to small molecule drugs as they offer superior specificity, lower toxicity, and easy synthesis. Here we present an approach that leverages the dramatic performance increase afforded by the recent arrival of GPU accelerated thermodynamic integration (TI). GPU TI facilitates very fast, highly accurate binding affinity optimization of peptides against therapeutic targets. We benchmarked TI predictions using published peptide binding optimization studies. Prediction of mutations involving charged side-chains was found to be less accurate than for non-charged, and use of a more complex 3-step TI protocol was found to boost accuracy in these cases. Using the 3-step protocol for non-charged side-chains either had no effect or was detrimental. We use the benchmarked pipeline to optimize a peptide binding to our recently discovered cancer target: EME1. TI calculations predict beneficial mutations using both canonical and non-canonical amino acids. We validate these predictions using fluorescence polarization and confirm that binding affinity is increased. We further demonstrate that this increase translates to a significant reduction in pancreatic cancer cell viability.
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Affiliation(s)
- Michael Garton
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Carles Corbi-Verge
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Yuan Hu
- Merck & Co., Inc., Kenilworth, New Jersey.,Alkermes Inc., Waltham, Massachusetts
| | - Satra Nim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Nadya Tarasova
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland
| | | | - Philip M Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada
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5
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Abstract
![]()
Alchemical
free energy methods have gained much importance recently
from several reports of improved ligand–protein binding affinity
predictions based on their implementation using molecular dynamics
simulations. A large number of variants of such methods implementing
different accelerated sampling techniques and free energy estimators
are available, each claimed to be better than the others in its own
way. However, the key features of reproducibility and quantification
of associated uncertainties in such methods have barely been discussed.
Here, we apply a systematic protocol for uncertainty quantification
to a number of popular alchemical free energy methods, covering both
absolute and relative free energy predictions. We show that a reliable
measure of error estimation is provided by ensemble simulation—an
ensemble of independent MD simulations—which applies irrespective
of the free energy method. The need to use ensemble methods is fundamental
and holds regardless of the duration of time of the molecular dynamics
simulations performed.
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Affiliation(s)
- Agastya P Bhati
- Centre for Computational Science, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom
| | - Shunzhou Wan
- Centre for Computational Science, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom
| | - Yuan Hu
- Modeling and Informatics , Merck & Co., Inc. , 2000 Galloping Hill Road , Kenilworth , New Jersey 07033 , United States
| | - Brad Sherborne
- Modeling and Informatics , Merck & Co., Inc. , 2000 Galloping Hill Road , Kenilworth , New Jersey 07033 , United States
| | - Peter V Coveney
- Centre for Computational Science, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom
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6
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Sawyer TK, Partridge AW, Kaan HYK, Juang YC, Lim S, Johannes C, Yuen TY, Verma C, Kannan S, Aronica P, Tan YS, Sherborne B, Ha S, Hochman J, Chen S, Surdi L, Peier A, Sauvagnat B, Dandliker PJ, Brown CJ, Ng S, Ferrer F, Lane DP. Macrocyclic α helical peptide therapeutic modality: A perspective of learnings and challenges. Bioorg Med Chem 2018; 26:2807-2815. [PMID: 29598901 DOI: 10.1016/j.bmc.2018.03.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/03/2018] [Accepted: 03/06/2018] [Indexed: 12/20/2022]
Abstract
Macrocyclic α-helical peptides have emerged as a compelling new therapeutic modality to tackle targets confined to the intracellular compartment. Within the scope of hydrocarbon-stapling there has been significant progress to date, including the first stapled α-helical peptide to enter into clinical trials. The principal design concept of stapled α-helical peptides is to mimic a cognate (protein) ligand relative to binding its target via an α-helical interface. However, it was the proclivity of such stapled α-helical peptides to exhibit cell permeability and proteolytic stability that underscored their promise as unique macrocyclic peptide drugs for intracellular targets. This perspective highlights key learnings as well as challenges in basic research with respect to structure-based design, innovative chemistry, cell permeability and proteolytic stability that are essential to fulfill the promise of stapled α-helical peptide drug development.
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7
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Fradera X, Verras A, Hu Y, Wang D, Wang H, Fells JI, Armacost KA, Crespo A, Sherborne B, Wang H, Peng Z, Gao YD. Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016. J Comput Aided Mol Des 2017; 32:113-127. [PMID: 28913710 DOI: 10.1007/s10822-017-0053-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 06/02/2017] [Accepted: 08/29/2017] [Indexed: 10/18/2022]
Abstract
We describe the performance of multiple pose prediction methods for the D3R 2016 Grand Challenge. The pose prediction challenge includes 36 ligands, which represent 4 chemotypes and some miscellaneous structures against the FXR ligand binding domain. In this study we use a mix of fully automated methods as well as human-guided methods with considerations of both the challenge data and publicly available data. The methods include ensemble docking, colony entropy pose prediction, target selection by molecular similarity, molecular dynamics guided pose refinement, and pose selection by visual inspection. We evaluated the success of our predictions by method, chemotype, and relevance of publicly available data. For the overall data set, ensemble docking, visual inspection, and molecular dynamics guided pose prediction performed the best with overall mean RMSDs of 2.4, 2.2, and 2.2 Å respectively. For several individual challenge molecules, the best performing method is evaluated in light of that particular ligand. We also describe the protein, ligand, and public information data preparations that are typical of our binding mode prediction workflow.
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Affiliation(s)
- Xavier Fradera
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA, 02215, USA.
| | - Andreas Verras
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA.
| | - Yuan Hu
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| | - Deping Wang
- Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA, 19486, USA
| | - Hongwu Wang
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| | - James I Fells
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| | - Kira A Armacost
- Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA, 19486, USA
| | - Alejandro Crespo
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| | - Brad Sherborne
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| | - Huijun Wang
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| | - Zhengwei Peng
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
| | - Ying-Duo Gao
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033-1310, USA
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8
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Walker SS, Labroli M, Painter RE, Wiltsie J, Sherborne B, Murgolo N, Sher X, Mann P, Zuck P, Garlisi CG, Su J, Kargman S, Xiao L, Scapin G, Salowe S, Devito K, Sheth P, Buist N, Tan CM, Black TA, Roemer T. Antibacterial small molecules targeting the conserved TOPRIM domain of DNA gyrase. PLoS One 2017; 12:e0180965. [PMID: 28700746 PMCID: PMC5507300 DOI: 10.1371/journal.pone.0180965] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/23/2017] [Indexed: 12/21/2022] Open
Abstract
To combat the threat of antibiotic-resistant Gram-negative bacteria, novel agents that circumvent established resistance mechanisms are urgently needed. Our approach was to focus first on identifying bioactive small molecules followed by chemical lead prioritization and target identification. Within this annotated library of bioactives, we identified a small molecule with activity against efflux-deficient Escherichia coli and other sensitized Gram-negatives. Further studies suggested that this compound inhibited DNA replication and selection for resistance identified mutations in a subunit of E. coli DNA gyrase, a type II topoisomerase. Our initial compound demonstrated weak inhibition of DNA gyrase activity while optimized compounds demonstrated significantly improved inhibition of E. coli and Pseudomonas aeruginosa DNA gyrase and caused cleaved complex stabilization, a hallmark of certain bactericidal DNA gyrase inhibitors. Amino acid substitutions conferring resistance to this new class of DNA gyrase inhibitors reside exclusively in the TOPRIM domain of GyrB and are not associated with resistance to the fluoroquinolones, suggesting a novel binding site for a gyrase inhibitor.
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Affiliation(s)
- Scott S. Walker
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
- * E-mail:
| | - Marc Labroli
- Merck & Co., Inc., West Point, Pennsylvania, United States of America
| | | | - Judyann Wiltsie
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Brad Sherborne
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Nicholas Murgolo
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Xinwei Sher
- Merck & Co., Inc., Boston, Massachusetts, United States of America
| | - Paul Mann
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Paul Zuck
- Merck & Co., Inc., West Point, Pennsylvania, United States of America
| | | | - Jing Su
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Stacia Kargman
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Li Xiao
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Giovanna Scapin
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Scott Salowe
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Kristine Devito
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Payal Sheth
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Nichole Buist
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | | | - Todd A. Black
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Terry Roemer
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
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9
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Lee TS, Hu Y, Sherborne B, Guo Z, York DM. Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration. J Chem Theory Comput 2017; 13:3077-3084. [PMID: 28618232 DOI: 10.1021/acs.jctc.7b00102] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report the implementation of the thermodynamic integration method on the pmemd module of the AMBER 16 package on GPUs (pmemdGTI). The pmemdGTI code typically delivers over 2 orders of magnitude of speed-up relative to a single CPU core for the calculation of ligand-protein binding affinities with no statistically significant numerical differences and thus provides a powerful new tool for drug discovery applications.
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Affiliation(s)
- Tai-Sung Lee
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States
| | - Yuan Hu
- Department of Chemistry, Modeling and Informatics, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Brad Sherborne
- Department of Chemistry, Modeling and Informatics, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Zhuyan Guo
- Department of Chemistry, Modeling and Informatics, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States
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10
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Howe JA, Wang H, Fischmann TO, Balibar CJ, Xiao L, Galgoci AM, Malinverni JC, Mayhood T, Villafania A, Nahvi A, Murgolo N, Barbieri CM, Mann PA, Carr D, Xia E, Zuck P, Riley D, Painter RE, Walker SS, Sherborne B, de Jesus R, Pan W, Plotkin MA, Wu J, Rindgen D, Cummings J, Garlisi CG, Zhang R, Sheth PR, Gill CJ, Tang H, Roemer T. Selective small-molecule inhibition of an RNA structural element. Nature 2015; 526:672-7. [PMID: 26416753 DOI: 10.1038/nature15542] [Citation(s) in RCA: 270] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/04/2015] [Indexed: 02/06/2023]
Abstract
Riboswitches are non-coding RNA structures located in messenger RNAs that bind endogenous ligands, such as a specific metabolite or ion, to regulate gene expression. As such, riboswitches serve as a novel, yet largely unexploited, class of emerging drug targets. Demonstrating this potential, however, has proven difficult and is restricted to structurally similar antimetabolites and semi-synthetic analogues of their cognate ligand, thus greatly restricting the chemical space and selectivity sought for such inhibitors. Here we report the discovery and characterization of ribocil, a highly selective chemical modulator of bacterial riboflavin riboswitches, which was identified in a phenotypic screen and acts as a structurally distinct synthetic mimic of the natural ligand, flavin mononucleotide, to repress riboswitch-mediated ribB gene expression and inhibit bacterial cell growth. Our findings indicate that non-coding RNA structural elements may be more broadly targeted by synthetic small molecules than previously expected.
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Affiliation(s)
- John A Howe
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Hao Wang
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | | | - Carl J Balibar
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Li Xiao
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | | | | | - Todd Mayhood
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | | | - Ali Nahvi
- Merck Research Laboratories, West Point, Pennsylvania 19486, USA
| | | | | | - Paul A Mann
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Donna Carr
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Ellen Xia
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Paul Zuck
- Merck Research Laboratories, North Wales, Pennsylvania 19454, USA
| | - Dan Riley
- Merck Research Laboratories, North Wales, Pennsylvania 19454, USA
| | | | - Scott S Walker
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Brad Sherborne
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | | | - Weidong Pan
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | | | - Jin Wu
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Diane Rindgen
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - John Cummings
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | | | - Rumin Zhang
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Payal R Sheth
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Charles J Gill
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Haifeng Tang
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
| | - Terry Roemer
- Merck Research Laboratories, Kenilworth, New Jersey 07033, USA
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11
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Seganish WM, Fischmann TO, Sherborne B, Matasi J, Lavey B, McElroy WT, Tulshian D, Tata J, Sondey C, Garlisi CG, Devito K, Fossetta J, Lundell D, Niu X. Discovery and Structure Enabled Synthesis of 2,6-Diaminopyrimidin-4-one IRAK4 Inhibitors. ACS Med Chem Lett 2015; 6:942-7. [PMID: 26288698 DOI: 10.1021/acsmedchemlett.5b00279] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 07/09/2015] [Accepted: 07/12/2015] [Indexed: 11/28/2022] Open
Abstract
We report the identification and synthesis of a series of aminopyrimidin-4-one IRAK4 inhibitors. Through high throughput screening, an aminopyrimidine hit was identified and modified via structure enabled design to generate a new, potent, and kinase selective pyrimidin-4-one chemotype. This chemotype is exemplified by compound 16, which has potent IRAK4 inhibition activity (IC50 = 27 nM) and excellent kinase selectivity (>100-fold against 99% of 111 tested kinases), and compound 31, which displays potent IRAK4 activity (IC50 = 93 nM) and good rat bioavailability (F = 42%).
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Affiliation(s)
- W. Michael Seganish
- Discovery Chemistry, ‡Structural Sciences, §Computational Chemistry, ∥In Vitro Pharmacology, and ⊥Respiratory
and Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Thierry O. Fischmann
- Discovery Chemistry, ‡Structural Sciences, §Computational Chemistry, ∥In Vitro Pharmacology, and ⊥Respiratory
and Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Brad Sherborne
- Discovery Chemistry, ‡Structural Sciences, §Computational Chemistry, ∥In Vitro Pharmacology, and ⊥Respiratory
and Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Julius Matasi
- Discovery Chemistry, ‡Structural Sciences, §Computational Chemistry, ∥In Vitro Pharmacology, and ⊥Respiratory
and Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Brian Lavey
- Discovery Chemistry, ‡Structural Sciences, §Computational Chemistry, ∥In Vitro Pharmacology, and ⊥Respiratory
and Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - William T. McElroy
- Discovery Chemistry, ‡Structural Sciences, §Computational Chemistry, ∥In Vitro Pharmacology, and ⊥Respiratory
and Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Deen Tulshian
- Discovery Chemistry, ‡Structural Sciences, §Computational Chemistry, ∥In Vitro Pharmacology, and ⊥Respiratory
and Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - James Tata
- Discovery Chemistry, ‡Structural Sciences, §Computational Chemistry, ∥In Vitro Pharmacology, and ⊥Respiratory
and Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Christopher Sondey
- Discovery Chemistry, ‡Structural Sciences, §Computational Chemistry, ∥In Vitro Pharmacology, and ⊥Respiratory
and Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Charles G. Garlisi
- Discovery Chemistry, ‡Structural Sciences, §Computational Chemistry, ∥In Vitro Pharmacology, and ⊥Respiratory
and Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Kristine Devito
- Discovery Chemistry, ‡Structural Sciences, §Computational Chemistry, ∥In Vitro Pharmacology, and ⊥Respiratory
and Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - James Fossetta
- Discovery Chemistry, ‡Structural Sciences, §Computational Chemistry, ∥In Vitro Pharmacology, and ⊥Respiratory
and Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Daniel Lundell
- Discovery Chemistry, ‡Structural Sciences, §Computational Chemistry, ∥In Vitro Pharmacology, and ⊥Respiratory
and Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xiaoda Niu
- Discovery Chemistry, ‡Structural Sciences, §Computational Chemistry, ∥In Vitro Pharmacology, and ⊥Respiratory
and Immunology, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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12
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Mann PA, Müller A, Xiao L, Pereira PM, Yang C, Ho Lee S, Wang H, Trzeciak J, Schneeweis J, dos Santos MM, Murgolo N, She X, Gill C, Balibar CJ, Labroli M, Su J, Flattery A, Sherborne B, Maier R, Tan CM, Black T, Önder K, Kargman S, Monsma FJ, Pinho MG, Schneider T, Roemer T. Murgocil is a highly bioactive staphylococcal-specific inhibitor of the peptidoglycan glycosyltransferase enzyme MurG. ACS Chem Biol 2013; 8:2442-51. [PMID: 23957438 DOI: 10.1021/cb400487f] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Modern medicine is founded on the discovery of penicillin and subsequent small molecules that inhibit bacterial peptidoglycan (PG) and cell wall synthesis. However, the discovery of new chemically and mechanistically distinct classes of PG inhibitors has become exceedingly rare, prompting speculation that intracellular enzymes involved in PG precursor synthesis are not 'druggable' targets. Here, we describe a β-lactam potentiation screen to identify small molecules that augment the activity of β-lactams against methicillin-resistant Staphylococcus aureus (MRSA) and mechanistically characterize a compound resulting from this screen, which we have named murgocil. We provide extensive genetic, biochemical, and structural modeling data demonstrating both in vitro and in whole cells that murgocil specifically inhibits the intracellular membrane-associated glycosyltransferase, MurG, which synthesizes the lipid II PG substrate that penicillin binding proteins (PBPs) polymerize and cross-link into the cell wall. Further, we demonstrate that the chemical synergy and cidality achieved between murgocil and the β-lactam imipenem is mediated through MurG dependent localization of PBP2 to the division septum. Collectively, these data validate our approach to rationally identify new target-specific bioactive β-lactam potentiation agents and demonstrate that murgocil now serves as a highly selective and potent chemical probe to assist our understanding of PG biosynthesis and cell wall biogenesis across Staphylococcal species.
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Affiliation(s)
- Paul A. Mann
- Infectious
Disease Research, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Anna Müller
- Institute
of Medical Microbiology, Immunology and Parasitology—Pharmaceutical
Microbiology Section, University of Bonn, Bonn, Germany
| | - Li Xiao
- Computational
Chemistry, Global Structure Chemistry, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Pedro M. Pereira
- Laboratory
of Bacterial Cell Biology, Instituto de Tecnologia Química
e Biológica, Universidade Nova de Lisboa, Avenida da República, 2781-901 Oeiras, Portugal
| | - Christine Yang
- Medicinal
Chemistry, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Sang Ho Lee
- Infectious
Disease Research, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Hao Wang
- Infectious
Disease Research, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Joanna Trzeciak
- Infectious
Disease Research, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Jonathan Schneeweis
- In Vitro Pharmacology, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Margarida Moreira dos Santos
- Laboratory
of Bacterial Cell Biology, Instituto de Tecnologia Química
e Biológica, Universidade Nova de Lisboa, Avenida da República, 2781-901 Oeiras, Portugal
| | - Nicholas Murgolo
- Research
Solutions, Bioinformatics, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Xinwei She
- Informatics
IT, Merck Inc., Boston, Massachusetts 02110, United States
| | - Charles Gill
- In Vivo Pharmacology, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Carl J. Balibar
- Infectious
Disease Research, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Marc Labroli
- Medicinal
Chemistry, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Jing Su
- Medicinal
Chemistry, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Amy Flattery
- In Vivo Pharmacology, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Brad Sherborne
- Computational
Chemistry, Global Structure Chemistry, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Richard Maier
- Procomcure Biotech GmbH, Krems a.d. Donau, Austria
- Division of Molecular
Dermatology, Department of Dermatology, Paracelsus Medical University, Salzburg, Austria
| | - Christopher M. Tan
- Infectious
Disease Research, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Todd Black
- Infectious
Disease Research, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Kamil Önder
- Procomcure Biotech GmbH, Krems a.d. Donau, Austria
- Division of Molecular
Dermatology, Department of Dermatology, Paracelsus Medical University, Salzburg, Austria
| | - Stacia Kargman
- In Vitro Pharmacology, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Frederick J Monsma
- In Vitro Pharmacology, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
| | - Mariana G. Pinho
- Laboratory
of Bacterial Cell Biology, Instituto de Tecnologia Química
e Biológica, Universidade Nova de Lisboa, Avenida da República, 2781-901 Oeiras, Portugal
| | - Tanja Schneider
- Institute
of Medical Microbiology, Immunology and Parasitology—Pharmaceutical
Microbiology Section, University of Bonn, Bonn, Germany
- German Centre for Infection Research (DZIF), partner site
Bonn-Cologne, Bonn, Germany
| | - Terry Roemer
- Infectious
Disease Research, Merck Research Laboratories, Kenilworth, New Jersey 07033, United States
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13
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Urich R, Wishart G, Kiczun M, Richters A, Tidten-Luksch N, Rauh D, Sherborne B, Wyatt PG, Brenk R. De novo design of protein kinase inhibitors by in silico identification of hinge region-binding fragments. ACS Chem Biol 2013; 8:1044-52. [PMID: 23534475 PMCID: PMC3833278 DOI: 10.1021/cb300729y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [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] [Indexed: 01/09/2023]
Abstract
![]()
Protein kinases constitute an attractive
family of enzyme targets
with high relevance to cell and disease biology. Small molecule inhibitors
are powerful tools to dissect and elucidate the function of kinases
in chemical biology research and to serve as potential starting points
for drug discovery. However, the discovery and development of novel
inhibitors remains challenging. Here, we describe a structure-based de novo design approach that generates novel, hinge-binding
fragments that are synthetically feasible and can be elaborated to
small molecule libraries. Starting from commercially available compounds,
core fragments were extracted, filtered for pharmacophoric properties
compatible with hinge-region binding, and docked into a panel of protein
kinases. Fragments with a high consensus score were subsequently short-listed
for synthesis. Application of this strategy led to a number of core
fragments with no previously reported activity against kinases. Small
libraries around the core fragments were synthesized, and representative
compounds were tested against a large panel of protein kinases and
subjected to co-crystallization experiments. Each of the tested compounds
was active against at least one kinase, but not all kinases in the
panel were inhibited. A number of compounds showed high ligand efficiencies
for therapeutically relevant kinases; among them were MAPKAP-K3, SRPK1,
SGK1, TAK1, and GCK for which only few inhibitors are reported in
the literature.
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Affiliation(s)
- Robert Urich
- Drug Discovery Unit (DDU), Division
of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Sir James Black Centre, DD1 5EH,
U.K
| | - Grant Wishart
- Department of Chemistry, MSD, Newhouse, Lanarkshire, ML1 5SH, U.K
| | - Michael Kiczun
- Department of Chemistry, MSD, Newhouse, Lanarkshire, ML1 5SH, U.K
| | - André Richters
- Fakultät Chemie - Chemische
Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Naomi Tidten-Luksch
- Drug Discovery Unit (DDU), Division
of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Sir James Black Centre, DD1 5EH,
U.K
| | - Daniel Rauh
- Fakultät Chemie - Chemische
Biologie, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Brad Sherborne
- Department of Chemistry, MSD, Newhouse, Lanarkshire, ML1 5SH, U.K
| | - Paul G. Wyatt
- Drug Discovery Unit (DDU), Division
of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Sir James Black Centre, DD1 5EH,
U.K
| | - Ruth Brenk
- Institut für Pharmazie
und Biochemie, Johannes Gutenberg-Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
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14
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Kosugi T, Mitchell DR, Fujino A, Imai M, Kambe M, Kobayashi S, Makino H, Matsueda Y, Oue Y, Komatsu K, Imaizumi K, Sakai Y, Sugiura S, Takenouchi O, Unoki G, Yamakoshi Y, Cunliffe V, Frearson J, Gordon R, Harris CJ, Kalloo-Hosein H, Le J, Patel G, Simpson DJ, Sherborne B, Thomas PS, Suzuki N, Takimoto-Kamimura M, Kataoka KI. Correction to Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MAPKAP-K2) as an Antiinflammatory Target: Discovery and in Vivo Activity of Selective Pyrazolo[1,5- a]pyrimidine Inhibitors Using a Focused Library and Structure-Based Optimization Approach. J Med Chem 2012. [DOI: 10.1021/jm3013954] [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: 11/28/2022]
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15
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Kosugi T, Mitchell DR, Fujino A, Imai M, Kambe M, Kobayashi S, Makino H, Matsueda Y, Oue Y, Komatsu K, Imaizumi K, Sakai Y, Sugiura S, Takenouchi O, Unoki G, Yamakoshi Y, Cunliffe V, Frearson J, Gordon R, Harris CJ, Kalloo-Hosein H, Le J, Patel G, Simpson DJ, Sherborne B, Thomas PS, Suzuki N, Takimoto-Kamimura M, Kataoka KI. Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2) as an antiinflammatory target: discovery and in vivo activity of selective pyrazolo[1,5-a]pyrimidine inhibitors using a focused library and structure-based optimization approach. J Med Chem 2012; 55:6700-15. [PMID: 22746295 DOI: 10.1021/jm300411k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A novel class of mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2) inhibitors was discovered through screening a kinase-focused library. A homology model of MAPKAP-K2 was generated and used to guide the initial SAR studies and to rationalize the observed selectivity over CDK2. An X-ray crystal structure of a compound from the active series bound to crystalline MAPKAP-K2 confirmed the predicted binding mode. This has enabled the discovery of a series of pyrazolo[1,5-a]pyrimidine derivatives showing good in vitro cellular potency as anti-TNF-α agents and in vivo efficacy in a mouse model of endotoxin shock.
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Affiliation(s)
- Tomomi Kosugi
- Teijin Institute for Bio-medical Research, Teijin Pharma Ltd. , Hino, Tokyo 191-8512, Japan
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16
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Sherborne B. Free-Wilson in the 21st Century – evolution of a versatile toolkit for SAR analysis. J Cheminform 2011. [PMCID: PMC3083602 DOI: 10.1186/1758-2946-3-s1-p6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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17
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Brown AR, Bosies M, Cameron H, Clark J, Cowley A, Craighead M, Elmore MA, Firth A, Goodwin R, Goutcher S, Grant E, Grassie M, Grove SJ, Hamilton NM, Hampson H, Hillier A, Ho KK, Kiczun M, Kingsbury C, Kultgen SG, Littlewood PT, Lusher SJ, MacDonald S, McIntosh L, McIntyre T, Mistry A, Morphy JR, Nimz O, Ohlmeyer M, Pick J, Rankovic Z, Sherborne B, Smith A, Speake M, Spinks G, Thomson F, Watson L, Weston M. Discovery and optimisation of a selective non-steroidal glucocorticoid receptor antagonist. Bioorg Med Chem Lett 2011; 21:137-40. [DOI: 10.1016/j.bmcl.2010.11.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 11/09/2010] [Accepted: 11/09/2010] [Indexed: 10/18/2022]
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18
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Ray P, Wright J, Adam J, Bennett J, Boucharens S, Black D, Cook A, Brown AR, Epemolu O, Fletcher D, Haunso A, Huggett M, Jones P, Laats S, Lyons A, Mestres J, de Man J, Morphy R, Rankovic Z, Sherborne B, Sherry L, van Straten N, Westwood P, Zaman GZ. Fragment-based discovery of 6-substituted isoquinolin-1-amine based ROCK-I inhibitors. Bioorg Med Chem Lett 2011; 21:97-101. [DOI: 10.1016/j.bmcl.2010.11.060] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 11/12/2010] [Accepted: 11/15/2010] [Indexed: 12/20/2022]
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19
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Zhao YH, Abraham MH, Le J, Hersey A, Luscombe CN, Beck G, Sherborne B, Cooper I. Evaluation of rat intestinal absorption data and correlation with human intestinal absorption. Eur J Med Chem 2003; 38:233-43. [PMID: 12667690 DOI: 10.1016/s0223-5234(03)00015-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [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: 01/01/2023]
Abstract
The absorption of 111 drug and drug-like compounds was evaluated from 111 references based on the ratio of urinary excretion of drugs following oral and intravenous administration to intact rats and biliary excretion of bile duct-cannulated rats. Ninety-eight drug compounds for which both human and rat absorption data were available were selected for correlation analysis between the human and rat absorption. The result shows that the extent of absorption in these two species is similar. For 94% of the drugs the absorption difference between humans and rats is less than 20% and for 98% of drugs the difference is less than 30%. There is only one drug for which human absorption is significantly different from rat absorption. The standard deviation is 11% between human and rat absorption. The linear relationship between human and rat absorption forced through the origin, as determined by least squares regression, is %Absorption (human)=0.997%Absorption (rat) (n=98, SD=11). It is suggested that the absorption in rats could be used as an alternative method to human absorption in pre-clinical oral absorption studies.
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Affiliation(s)
- Yuan H Zhao
- Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ, London, UK
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20
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Abstract
PURPOSE To classify the dissolution and diffusion rate-limited drugs and establish quantitative relationships between absorption and molecular descriptors. METHODS Absorption consists of kinetic transit processes in which dissolution, diffusion, or perfusion processes can become the rate-limited step. The absorption data of 238 drugs have been classified into either dissolution or diffusion rate-limited based on an equilibrium method developed from solubility, dose, and percentage of absorption. A nonlinear absorption model derived from first-order kinetics has been developed to identify the relationship between percentage of drug absorption and molecular descriptors. RESULTS Regression analysis was performed between percentage of absorption and molecular descriptors. The descriptors used were ClogP, molecular polar surface area, the number of hydrogen-bonding acceptors and donors, and Abraham descriptors. Good relationships were found between absorption and Abraham descriptors or ClogP. CONCLUSIONS The absorption models can predict the following three BCS (Biopharmaceutics Classification Scheme) classes of compounds: class I, high solubility and high permeability; class III, high solubility and low permeability; class IV, low solubility and low permeability. The absorption models overpredict the absorption of class II, low solubility and high permeability compounds because dissolution is the rate-limited step of absorption.
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Affiliation(s)
- Yuan H Zhao
- Department of Chemistry, University College London, United Kingdom
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21
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Abstract
In order to investigate whether the main step in intestinal absorption in humans is dominated by partition or by diffusion, we have transformed % human intestinal absorption into a first-order rate constant, and have regressed the latter, as logk, against our solvation parameters. The obtained regression coefficients are compared with those for diffusion and partition processes. The coefficients in the logk equation are completely different to those for water/solvent partitions, but are very similar to those for processes (not involving transport through membranes) in which diffusion is the major step. It is suggested that the main step in the absorption process is diffusion through a stagnant mucus layer, together with transfer across the mucusmid R:membrane interface. It is further shown that for strong Bronsted acids and bases, the rate constant for absorption of ionic species is close to that for absorption of the corresponding neutral species, so that to a first approximation the % intestinal absorption can be calculated from properties of the neutral species.
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Affiliation(s)
- Michael H Abraham
- Department of Chemistry, University College London, 20 Gordon Street, WC1H OAJ, London, UK.
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22
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Zhao YH, Le J, Abraham MH, Hersey A, Eddershaw PJ, Luscombe CN, Butina D, Beck G, Sherborne B, Cooper I, Platts JA. Erratum: Evaluation of human intestinal absorption data and subsequent derivation of a quantitative structure–activity relationship (QSAR) with the Abraham descriptors. J Pharm Sci 2002. [DOI: 10.1002/jps.10118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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23
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Zhao YH, Le J, Abraham MH, Hersey A, Eddershaw PJ, Luscombe CN, Butina D, Beck G, Sherborne B, Cooper I, Platts JA, Boutina D. Evaluation of human intestinal absorption data and subsequent derivation of a quantitative structure–activity relationship (QSAR) with the Abraham descriptors. J Pharm Sci 2001; 90:749-84. [PMID: 11357178 DOI: 10.1002/jps.1031] [Citation(s) in RCA: 357] [Impact Index Per Article: 15.5] [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: 01/06/2023]
Abstract
The human intestinal absorption of 241 drugs was evaluated. Three main methods were used to determine the human intestinal absorption: bioavailability, percentage of urinary excretion of drug-related material following oral administration, and the ratio of cumulative urinary excretion of drug-related material following oral and intravenous administration. The general solvation equation developed by Abraham's group was used to model the human intestinal absorption data of 169 drugs we considered to have reliable data. The model contains five Abraham descriptors calculated by the ABSOLV program. The results show that Abraham descriptors can successfully predict human intestinal absorption if the human absorption data is carefully classified based on solubility and administration dose to humans.
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Affiliation(s)
- Y H Zhao
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
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Abraham RJ, Aboitiz N, Merrett J, Sherborne B, Whitcombe I. Conformational analysis. Part 34. An NMR investigation of the conformational equilibrium and intramolecular hydrogen bonding in nipecotic acid derivatives. ACTA ACUST UNITED AC 2000. [DOI: 10.1039/b007506j] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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