1
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Fraczkiewicz R, Quoc Nguyen H, Wu N, Kausch-Busies N, Grimbs S, Sommer K, Ter Laak A, Günther J, Wagner B, Reutlinger M. Best of both worlds: An expansion of the state of the art pK a model with data from three industrial partners. Mol Inform 2024:e202400088. [PMID: 39031889 DOI: 10.1002/minf.202400088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/11/2024] [Accepted: 05/12/2024] [Indexed: 07/22/2024]
Abstract
In a unique collaboration between Simulations Plus and several industrial partners, we were able to develop a new version 11.0 of the previously published in silico pKa model, S+pKa, with considerably improved prediction accuracy. The model's training set was vastly expanded by large amounts of experimental data obtained from F. Hoffmann-La Roche AG, Genentech Inc., and the Crop Science division of Bayer AG. The previous v7.0 of S+pKa was trained on data from public sources and the Pharmaceutical division of Bayer AG. The model has shown dramatic improvements in predictive accuracy when externally validated on three new contributor compound sets. Less expected was v11.0's improvement in prediction on new compounds developed at Bayer Pharma after v7.0 was released (2013-2023), even without contributing additional data to v11.0. We illustrate chemical space coverage by chemistries encountered in the five domains, public and industrial, outline model construction, and discuss factors contributing to model's success.
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Affiliation(s)
| | - Huy Quoc Nguyen
- Genentech Inc., Discovery Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Newton Wu
- Genentech Inc., Discovery Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Sergio Grimbs
- Bayer AG, Research & Development, Crop Science, 40789, Monheim, Germany
| | - Kai Sommer
- Bayer AG, Research & Development, Crop Science, 40789, Monheim, Germany
| | - Antonius Ter Laak
- Bayer AG, Research & Development, Pharmaceuticals, 13353, Berlin, Germany
| | - Judith Günther
- Bayer AG, Research & Development, Pharmaceuticals, 13353, Berlin, Germany
| | - Björn Wagner
- F. Hoffmann-La Roche AG, Roche Pharma Research and Early Development, 4070, Basel, Switzerland
| | - Michael Reutlinger
- F. Hoffmann-La Roche AG, Roche Pharma Research and Early Development, 4070, Basel, Switzerland
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2
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Yang L, Skolnik S. Avoid missing pK as: High-throughput workflow using solution pH-metric in tandem with UV-metric measurements. J Pharm Biomed Anal 2023; 234:115530. [PMID: 37343451 DOI: 10.1016/j.jpba.2023.115530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/06/2023] [Accepted: 06/12/2023] [Indexed: 06/23/2023]
Abstract
We describe a new high-throughput automated pKa workflow using potentiometry starting with 10 mM DMSO stock (solution pH-metric). Two approaches using either neat DMSO stock solution or removal of DMSO were evaluated with different sample amounts and cosolvent schemes. These were validated against traditional potentiometric measurements for optimal conditions. Further, we detail how high throughput solution pH-metric experiments are performed in tandem with established UV-metric measurements to capitalize on the advantages of both approaches. This new workflow maintains the sample and time savings required for measuring a large number of samples in a drug discovery setting, while avoiding "missing pKas" due to lack of sufficient UV chromophores. The combination of the two assays is key to tackle the challenges of low solubility, overlapping pKas, and preliminary assignment of pKas for Structure-Activity Relationship (SAR) understanding.
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Affiliation(s)
- Linhong Yang
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
| | - Suzanne Skolnik
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
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3
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Isert C, Kromann JC, Stiefl N, Schneider G, Lewis RA. Machine Learning for Fast, Quantum Mechanics-Based Approximation of Drug Lipophilicity. ACS OMEGA 2023; 8:2046-2056. [PMID: 36687099 PMCID: PMC9850743 DOI: 10.1021/acsomega.2c05607] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Lipophilicity, as measured by the partition coefficient between octanol and water (log P), is a key parameter in early drug discovery research. However, measuring log P experimentally is difficult for specific compounds and log P ranges. The resulting lack of reliable experimental data impedes development of accurate in silico models for such compounds. In certain discovery projects at Novartis focused on such compounds, a quantum mechanics (QM)-based tool for log P estimation has emerged as a valuable supplement to experimental measurements and as a preferred alternative to existing empirical models. However, this QM-based approach incurs a substantial computational cost, limiting its applicability to small series and prohibiting quick, interactive ideation. This work explores a set of machine learning models (Random Forest, Lasso, XGBoost, Chemprop, and Chemprop3D) to learn calculated log P values on both a public data set and an in-house data set to obtain a computationally affordable, QM-based estimation of drug lipophilicity. The message-passing neural network model Chemprop emerged as the best performing model with mean absolute errors of 0.44 and 0.34 log units for scaffold split test sets of the public and in-house data sets, respectively. Analysis of learning curves suggests that a further decrease in the test set error can be achieved by increasing the training set size. While models directly trained on experimental data perform better at approximating experimentally determined log P values than models trained on calculated values, we discuss the potential advantages of using calculated log P values going beyond the limits of experimental quantitation. We analyze the impact of the data set splitting strategy and gain insights into model failure modes. Potential use cases for the presented models include pre-screening of large compound collections and prioritization of compounds for full QM calculations.
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Affiliation(s)
- Clemens Isert
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093Zurich, Switzerland
- Novartis
Institutes for BioMedical Research, 4056Basel, Switzerland
| | - Jimmy C. Kromann
- Novartis
Institutes for BioMedical Research, 4056Basel, Switzerland
| | - Nikolaus Stiefl
- Novartis
Institutes for BioMedical Research, 4056Basel, Switzerland
| | - Gisbert Schneider
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093Zurich, Switzerland
- ETH
Singapore SEC Ltd., 1
CREATE Way, #06-01 CREATE Tower138602, Singapore, Singapore
| | - Richard A. Lewis
- Novartis
Institutes for BioMedical Research, 4056Basel, Switzerland
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4
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Hamzic S, Lewis R, Desrayaud S, Soylu C, Fortunato M, Gerebtzoff G, Rodríguez-Pérez R. Predicting In Vivo Compound Brain Penetration Using Multi-task Graph Neural Networks. J Chem Inf Model 2022; 62:3180-3190. [PMID: 35738004 DOI: 10.1021/acs.jcim.2c00412] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Assessing whether compounds penetrate the brain can become critical in drug discovery, either to prevent adverse events or to reach the biological target. Generally, pre-clinical in vivo studies measuring the ratio of brain and blood concentrations (Kp) are required to estimate the brain penetration potential of a new drug entity. In this work, we developed machine learning models to predict in vivo compound brain penetration (as LogKp) from chemical structure. Our results show the benefit of including in vitro experimental data as auxiliary tasks in multi-task graph neural network (MT-GNN) models. MT-GNNs outperformed single-task (ST) models solely trained on in vivo brain penetration data. The best-performing MT-GNN regression model achieved a coefficient of determination of 0.42 and a mean absolute error of 0.39 (2.5-fold) on a prospective validation set and outperformed all tested ST models. To facilitate decision-making, compounds were classified into brain-penetrant or non-penetrant, achieving a Matthew's correlation coefficient of 0.66. Taken together, our findings indicate that the inclusion of in vitro assay data as MT-GNN auxiliary tasks improves in vivo brain penetration predictions and prospective compound prioritization.
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Affiliation(s)
- Seid Hamzic
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Richard Lewis
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Sandrine Desrayaud
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Cihan Soylu
- Novartis Institutes for BioMedical Research Inc., 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Mike Fortunato
- Novartis Institutes for BioMedical Research Inc., 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Grégori Gerebtzoff
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Raquel Rodríguez-Pérez
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4002 Basel, Switzerland
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5
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Miethke M, Pieroni M, Weber T, Brönstrup M, Hammann P, Halby L, Arimondo PB, Glaser P, Aigle B, Bode HB, Moreira R, Li Y, Luzhetskyy A, Medema MH, Pernodet JL, Stadler M, Tormo JR, Genilloud O, Truman AW, Weissman KJ, Takano E, Sabatini S, Stegmann E, Brötz-Oesterhelt H, Wohlleben W, Seemann M, Empting M, Hirsch AKH, Loretz B, Lehr CM, Titz A, Herrmann J, Jaeger T, Alt S, Hesterkamp T, Winterhalter M, Schiefer A, Pfarr K, Hoerauf A, Graz H, Graz M, Lindvall M, Ramurthy S, Karlén A, van Dongen M, Petkovic H, Keller A, Peyrane F, Donadio S, Fraisse L, Piddock LJV, Gilbert IH, Moser HE, Müller R. Towards the sustainable discovery and development of new antibiotics. Nat Rev Chem 2021; 5:726-749. [PMID: 34426795 PMCID: PMC8374425 DOI: 10.1038/s41570-021-00313-1] [Citation(s) in RCA: 404] [Impact Index Per Article: 134.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 02/08/2023]
Abstract
An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations.
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Affiliation(s)
- Marcus Miethke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Marco Pieroni
- Food and Drug Department, University of Parma, Parma, Italy
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mark Brönstrup
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Department of Chemical Biology (CBIO), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Peter Hammann
- Infectious Diseases & Natural Product Research at EVOTEC, and Justus Liebig University Giessen, Giessen, Germany
| | - Ludovic Halby
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Paola B. Arimondo
- Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Institut Pasteur, UMR n°3523, CNRS, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotic Resistance Unit, Microbiology Department, Institut Pasteur, CNRS UMR3525, Paris, France
| | | | - Helge B. Bode
- Department of Biosciences, Goethe University Frankfurt, Frankfurt, Germany
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
| | - Rui Moreira
- Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Yanyan Li
- Unit MCAM, CNRS, National Museum of Natural History (MNHN), Paris, France
| | - Andriy Luzhetskyy
- Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Jean-Luc Pernodet
- Institute for Integrative Biology of the Cell (I2BC) & Microbiology Department, University of Paris-Saclay, Gif-sur-Yvette, France
| | - Marc Stadler
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Microbial Drugs (MWIS), Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | | | | | - Andrew W. Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Kira J. Weissman
- Molecular and Structural Enzymology Group, Université de Lorraine, CNRS, IMoPA, Nancy, France
| | - Eriko Takano
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, Manchester, United Kingdom
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Evi Stegmann
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Wolfgang Wohlleben
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Myriam Seemann
- Institute for Chemistry UMR 7177, University of Strasbourg/CNRS, ITI InnoVec, Strasbourg, France
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Brigitta Loretz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Claus-Michael Lehr
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
| | - Alexander Titz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Timo Jaeger
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Silke Alt
- German Center for Infection Research (DZIF), Braunschweig, Germany
| | | | | | - Andrea Schiefer
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Kenneth Pfarr
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Achim Hoerauf
- German Center for Infection Research (DZIF), Braunschweig, Germany
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Heather Graz
- Biophys Ltd., Usk, Monmouthshire, United Kingdom
| | - Michael Graz
- School of Law, University of Bristol, Bristol, United Kingdom
| | | | | | - Anders Karlén
- Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | | | - Hrvoje Petkovic
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken, Germany
| | | | | | - Laurent Fraisse
- Drugs for Neglected Diseases initiative (DNDi), Geneva, Switzerland
| | - Laura J. V. Piddock
- The Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Ian H. Gilbert
- Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, United Kingdom
| | - Heinz E. Moser
- Novartis Institutes for BioMedical Research (NIBR), Emeryville, CA USA
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
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6
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Lapointe G, Skepper CK, Holder LM, Armstrong D, Bellamacina C, Blais J, Bussiere D, Bian J, Cepura C, Chan H, Dean CR, De Pascale G, Dhumale B, Fisher LM, Fulsunder M, Kantariya B, Kim J, King S, Kossy L, Kulkarni U, Lakshman J, Leeds JA, Ling X, Lvov A, Ma S, Malekar S, McKenney D, Mergo W, Metzger L, Mhaske K, Moser HE, Mostafavi M, Namballa S, Noeske J, Osborne C, Patel A, Patel D, Patel T, Piechon P, Polyakov V, Prajapati K, Prosen KR, Reck F, Richie DL, Sanderson MR, Satasia S, Savani B, Selvarajah J, Sethuraman V, Shu W, Tashiro K, Thompson KV, Vaarla K, Vala L, Veselkov DA, Vo J, Vora B, Wagner T, Wedel L, Williams SL, Yendluri S, Yue Q, Yifru A, Zhang Y, Rivkin A. Discovery and Optimization of DNA Gyrase and Topoisomerase IV Inhibitors with Potent Activity against Fluoroquinolone-Resistant Gram-Positive Bacteria. J Med Chem 2021; 64:6329-6357. [PMID: 33929852 DOI: 10.1021/acs.jmedchem.1c00375] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Herein, we describe the discovery and optimization of a novel series that inhibits bacterial DNA gyrase and topoisomerase IV via binding to, and stabilization of, DNA cleavage complexes. Optimization of this series led to the identification of compound 25, which has potent activity against Gram-positive bacteria, a favorable in vitro safety profile, and excellent in vivo pharmacokinetic properties. Compound 25 was found to be efficacious against fluoroquinolone-sensitive Staphylococcus aureus infection in a mouse thigh model at lower doses than moxifloxacin. An X-ray crystal structure of the ternary complex formed by topoisomerase IV from Klebsiella pneumoniae, compound 25, and cleaved DNA indicates that this compound does not engage in a water-metal ion bridge interaction and forms no direct contacts with residues in the quinolone resistance determining region (QRDR). This suggests a structural basis for the reduced impact of QRDR mutations on antibacterial activity of 25 compared to fluoroquinolones.
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Affiliation(s)
- Guillaume Lapointe
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Colin K Skepper
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Lauren M Holder
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Duncan Armstrong
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Cornelia Bellamacina
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Johanne Blais
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Dirksen Bussiere
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jianwei Bian
- Novartis Global Drug Development, Pudong, Shanghai 201203, China
| | - Cody Cepura
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Helen Chan
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Charles R Dean
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Gianfranco De Pascale
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bhavesh Dhumale
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - L Mark Fisher
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, U.K
| | - Mangesh Fulsunder
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Bhavin Kantariya
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Julie Kim
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sean King
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Lauren Kossy
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Upendra Kulkarni
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jay Lakshman
- Novartis Global Drug Development, East Hanover, New Jersey 07936, United States
| | - Jennifer A Leeds
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Xiaolan Ling
- Novartis Global Drug Development, Pudong, Shanghai 201203, China
| | - Anatoli Lvov
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Sylvia Ma
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Swapnil Malekar
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - David McKenney
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Wosenu Mergo
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Louis Metzger
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Keshav Mhaske
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Heinz E Moser
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Mina Mostafavi
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sunil Namballa
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Jonas Noeske
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Colin Osborne
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Ashish Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Darshit Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Tushar Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Philippe Piechon
- Novartis Institutes for BioMedical Research, Basel 4002, Switzerland
| | - Valery Polyakov
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Krunal Prajapati
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Katherine R Prosen
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Folkert Reck
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Daryl L Richie
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Mark R Sanderson
- Randall Centre for Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, U.K
| | - Shailesh Satasia
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Bhautik Savani
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Jogitha Selvarajah
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, U.K
| | - Vijay Sethuraman
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Wei Shu
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Kyuto Tashiro
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Katherine V Thompson
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Krishniah Vaarla
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Lakhan Vala
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Dennis A Veselkov
- Randall Centre for Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, U.K
| | - Jason Vo
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bhavesh Vora
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Trixie Wagner
- Novartis Institutes for BioMedical Research, Basel 4002, Switzerland
| | - Laura Wedel
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sarah L Williams
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Satya Yendluri
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Qin Yue
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Aregahegn Yifru
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Yong Zhang
- Novartis Global Drug Development, Pudong, Shanghai 201203, China
| | - Alexey Rivkin
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
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7
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Suthers PF, Foster CJ, Sarkar D, Wang L, Maranas CD. Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms. Metab Eng 2020; 63:13-33. [PMID: 33310118 DOI: 10.1016/j.ymben.2020.11.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/13/2020] [Accepted: 11/27/2020] [Indexed: 12/16/2022]
Abstract
Understanding the governing principles behind organisms' metabolism and growth underpins their effective deployment as bioproduction chassis. A central objective of metabolic modeling is predicting how metabolism and growth are affected by both external environmental factors and internal genotypic perturbations. The fundamental concepts of reaction stoichiometry, thermodynamics, and mass action kinetics have emerged as the foundational principles of many modeling frameworks designed to describe how and why organisms allocate resources towards both growth and bioproduction. This review focuses on the latest algorithmic advancements that have integrated these foundational principles into increasingly sophisticated quantitative frameworks.
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Affiliation(s)
- Patrick F Suthers
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, USA
| | - Charles J Foster
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Debolina Sarkar
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Lin Wang
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, USA.
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8
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Velcicky J, Wilcken R, Cotesta S, Janser P, Schlapbach A, Wagner T, Piechon P, Villard F, Bouhelal R, Piller F, Harlfinger S, Stringer R, Fehlmann D, Kaupmann K, Littlewood-Evans A, Haffke M, Gommermann N. Discovery and Optimization of Novel SUCNR1 Inhibitors: Design of Zwitterionic Derivatives with a Salt Bridge for the Improvement of Oral Exposure. J Med Chem 2020; 63:9856-9875. [DOI: 10.1021/acs.jmedchem.0c01020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Juraj Velcicky
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Rainer Wilcken
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Simona Cotesta
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Philipp Janser
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Achim Schlapbach
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Trixie Wagner
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Philippe Piechon
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Frederic Villard
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Rochdi Bouhelal
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Fabian Piller
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | | | - Rowan Stringer
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | | | - Klemens Kaupmann
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | | | - Matthias Haffke
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Nina Gommermann
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
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9
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Skepper CK, Armstrong D, Balibar CJ, Bauer D, Bellamacina C, Benton BM, Bussiere D, De Pascale G, De Vicente J, Dean CR, Dhumale B, Fisher LM, Fuller J, Fulsunder M, Holder LM, Hu C, Kantariya B, Lapointe G, Leeds JA, Li X, Lu P, Lvov A, Ma S, Madhavan S, Malekar S, McKenney D, Mergo W, Metzger L, Moser HE, Mutnick D, Noeske J, Osborne C, Patel A, Patel D, Patel T, Prajapati K, Prosen KR, Reck F, Richie DL, Rico A, Sanderson MR, Satasia S, Sawyer WS, Selvarajah J, Shah N, Shanghavi K, Shu W, Thompson KV, Traebert M, Vala A, Vala L, Veselkov DA, Vo J, Wang M, Widya M, Williams SL, Xu Y, Yue Q, Zang R, Zhou B, Rivkin A. Topoisomerase Inhibitors Addressing Fluoroquinolone Resistance in Gram-Negative Bacteria. J Med Chem 2020; 63:7773-7816. [PMID: 32634310 DOI: 10.1021/acs.jmedchem.0c00347] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since their discovery over 5 decades ago, quinolone antibiotics have found enormous success as broad spectrum agents that exert their activity through dual inhibition of bacterial DNA gyrase and topoisomerase IV. Increasing rates of resistance, driven largely by target-based mutations in the GyrA/ParC quinolone resistance determining region, have eroded the utility and threaten the future use of this vital class of antibiotics. Herein we describe the discovery and optimization of a series of 4-(aminomethyl)quinolin-2(1H)-ones, exemplified by 34, that inhibit bacterial DNA gyrase and topoisomerase IV and display potent activity against ciprofloxacin-resistant Gram-negative pathogens. X-ray crystallography reveals that 34 occupies the classical quinolone binding site in the topoisomerase IV-DNA cleavage complex but does not form significant contacts with residues in the quinolone resistance determining region.
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Affiliation(s)
- Colin K Skepper
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Duncan Armstrong
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Carl J Balibar
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Daniel Bauer
- Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Cornelia Bellamacina
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bret M Benton
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Dirksen Bussiere
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Gianfranco De Pascale
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Javier De Vicente
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Charles R Dean
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bhavesh Dhumale
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - L Mark Fisher
- Molecular and Clinical Sciences Research Institute, St George's University of London, London SW17 0RE, U.K
| | - John Fuller
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Mangesh Fulsunder
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Lauren M Holder
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Cheng Hu
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bhavin Kantariya
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Guillaume Lapointe
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jennifer A Leeds
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Xiaolin Li
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Peichao Lu
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Anatoli Lvov
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Sylvia Ma
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Shravanthi Madhavan
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Swapnil Malekar
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - David McKenney
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Wosenu Mergo
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Louis Metzger
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Heinz E Moser
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Daniel Mutnick
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jonas Noeske
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Colin Osborne
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Ashish Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Darshit Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Tushar Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Krunal Prajapati
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Katherine R Prosen
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Folkert Reck
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Daryl L Richie
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alice Rico
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Mark R Sanderson
- Randall Centre for Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, U.K
| | - Shailesh Satasia
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - William S Sawyer
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jogitha Selvarajah
- Molecular and Clinical Sciences Research Institute, St George's University of London, London SW17 0RE, U.K
| | - Nirav Shah
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Kartik Shanghavi
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Wei Shu
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Katherine V Thompson
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Martin Traebert
- Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Anand Vala
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Lakhan Vala
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Dennis A Veselkov
- Randall Centre for Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, U.K
| | - Jason Vo
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Michael Wang
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Marcella Widya
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sarah L Williams
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Yongjin Xu
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Qin Yue
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Richard Zang
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bo Zhou
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alexey Rivkin
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
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10
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Lu Y, Anand S, Shirley W, Gedeck P, Kelley BP, Skolnik S, Rodde S, Nguyen M, Lindvall M, Jia W. Prediction of pKa Using Machine Learning Methods with Rooted Topological Torsion Fingerprints: Application to Aliphatic Amines. J Chem Inf Model 2019; 59:4706-4719. [DOI: 10.1021/acs.jcim.9b00498] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Yipin Lu
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Shankara Anand
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - William Shirley
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Peter Gedeck
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brian P. Kelley
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Suzanne Skolnik
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Stephane Rodde
- Novartis Institutes for Biomedical Research, Postfach, CH-4002 Basel, Switzerland
| | - Mai Nguyen
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mika Lindvall
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Weiping Jia
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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11
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Ruggiu F, Yang S, Simmons RL, Casarez A, Jones AK, Li C, Jansen JM, Moser HE, Dean CR, Reck F, Lindvall M. Size Matters and How You Measure It: A Gram-Negative Antibacterial Example Exceeding Typical Molecular Weight Limits. ACS Infect Dis 2019; 5:1688-1692. [PMID: 31478369 DOI: 10.1021/acsinfecdis.9b00256] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Monobactam antibiotic 1 is active against Gram-negative bacteria even though it has a higher molecular weight (MW) than the limit of 600 Da typically applied in designing such compounds. On the basis of 2D NMR data, the compound is able to adopt a compact conformation. The dimensions, projection area, and dipole moment derived from this conformation are compatible with porin permeation, as are locations of polar groups upon superimposition to the crystal structure of ampicillin bound to E. coli OmpF porin. Minimum inhibitory concentration (MIC) shifts in a porin knock-out strain are also consistent with 1 predominately permeating through porins. In conclusion, we describe a carefully characterized case of a molecule outside default design parameters where MW does not adequately represent the 3D shape more directly related to permeability. Leveraging 3D design criteria would open up additional chemical space currently underutilized due to limitations perceived in 2D.
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Affiliation(s)
- Fiorella Ruggiu
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Shengtian Yang
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Robert L. Simmons
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Anthony Casarez
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Adriana K. Jones
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Cindy Li
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Johanna M. Jansen
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Heinz E. Moser
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Charles R. Dean
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Folkert Reck
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mika Lindvall
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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12
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Kalliokoski T, Sinervo K. Predicting pK
a
for Small Molecules on Public and In‐house Datasets Using Fast Prediction Methods Combined with Data Fusion. Mol Inform 2019; 38:e1800163. [DOI: 10.1002/minf.201800163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/06/2019] [Indexed: 11/05/2022]
Affiliation(s)
| | - Kai Sinervo
- Orion Pharma Orionintie 1 A 02101 Espoo Finland
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13
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Pracht P, Wilcken R, Udvarhelyi A, Rodde S, Grimme S. High accuracy quantum-chemistry-based calculation and blind prediction of macroscopic pKa values in the context of the SAMPL6 challenge. J Comput Aided Mol Des 2018; 32:1139-1149. [PMID: 30141103 DOI: 10.1007/s10822-018-0145-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/02/2018] [Indexed: 12/14/2022]
Abstract
Recent advances in the development of low-cost quantum chemical methods have made the prediction of conformational preferences and physicochemical properties of medium-sized drug-like molecules routinely feasible, with significant potential to advance drug discovery. In the context of the SAMPL6 challenge, macroscopic pKa values were blindly predicted for a set of 24 of such molecules. In this paper we present two similar quantum chemical based approaches based on the high accuracy calculation of standard reaction free energies and the subsequent determination of those pKa values via a linear free energy relationship. Both approaches use extensive conformational sampling and apply hybrid and double-hybrid density functional theory with continuum solvation to calculate free energies. The blindly calculated macroscopic pKa values were in excellent agreement with the experiment.
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Affiliation(s)
- Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115, Bonn, Germany
| | - Rainer Wilcken
- Novartis Institutes for Biomedical Research, 4002, Basel, Switzerland.
| | - Anikó Udvarhelyi
- Novartis Pharma AG, Technical Research and Development, 4002, Basel, Switzerland
| | - Stephane Rodde
- Novartis Institutes for Biomedical Research, 4002, Basel, Switzerland
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115, Bonn, Germany.
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14
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Wagman AS, Boyce RS, Brown SP, Fang E, Goff D, Jansen JM, Le VP, Levine BH, Ng SC, Ni ZJ, Nuss JM, Pfister KB, Ramurthy S, Renhowe PA, Ring DB, Shu W, Subramanian S, Zhou XA, Shafer CM, Harrison SD, Johnson KW, Bussiere DE. Synthesis, Binding Mode, and Antihyperglycemic Activity of Potent and Selective (5-Imidazol-2-yl-4-phenylpyrimidin-2-yl)[2-(2-pyridylamino)ethyl]amine Inhibitors of Glycogen Synthase Kinase 3. J Med Chem 2017; 60:8482-8514. [DOI: 10.1021/acs.jmedchem.7b00922] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Allan S. Wagman
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Rustum S. Boyce
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Sean P. Brown
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Eric Fang
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Dane Goff
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Johanna M. Jansen
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Vincent P. Le
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Barry H. Levine
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Simon C. Ng
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Zhi-Jie Ni
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - John M. Nuss
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Keith B. Pfister
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Savithri Ramurthy
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Paul A. Renhowe
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - David B. Ring
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wei Shu
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Sharadha Subramanian
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Xiaohui A. Zhou
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Cynthia M. Shafer
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Stephen D. Harrison
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kirk W. Johnson
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Dirksen E. Bussiere
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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15
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Yan S, Shaw DE, Yang L, Sandham DA, Healy MP, Reilly J, Wang B. Interactions between β2-Adrenoceptor Ligands and Membrane: Atomic-Level Insights from Magic-Angle Spinning NMR. J Med Chem 2017; 60:6867-6879. [PMID: 28703592 DOI: 10.1021/acs.jmedchem.7b00205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To understand the relationship between structural properties of the β2-adrenoceptor ligands and their interactions with membranes, we have investigated the location and distribution of five β2 agonists with distinct clinical durations and onsets of action (indacaterol, two indacaterol analogues, salmeterol and formoterol) in monounsaturated model membranes using magic angle spinning NMR to measure these interactions through both 1H nuclear Overhauser enhancement (NOE) and paramagnetic relaxation enhancement (PRE) techniques. The hydrophilic aromatic groups of all five β2 agonists show maximum distribution in the lipid/water interface, but distinct location and dynamic behavior were observed for the lipophilic aromatic rings. Our study elucidates at atomic level that the hydrophobicity and substitution geometry of lipophilic groups play important roles in compound-lipid interactions.
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Affiliation(s)
- Si Yan
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , Cambridge, Massachusetts 02139, United States
| | - Duncan E Shaw
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , Cambridge, Massachusetts 02139, United States
| | - Linhong Yang
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , Cambridge, Massachusetts 02139, United States
| | - David A Sandham
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , Cambridge, Massachusetts 02139, United States
| | - Mark P Healy
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , Cambridge, Massachusetts 02139, United States
| | - John Reilly
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , Cambridge, Massachusetts 02139, United States
| | - Bing Wang
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , Cambridge, Massachusetts 02139, United States
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16
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Lingel A, Sendzik M, Huang Y, Shultz MD, Cantwell J, Dillon MP, Fu X, Fuller J, Gabriel T, Gu J, Jiang X, Li L, Liang F, McKenna M, Qi W, Rao W, Sheng X, Shu W, Sutton J, Taft B, Wang L, Zeng J, Zhang H, Zhang M, Zhao K, Lindvall M, Bussiere DE. Structure-Guided Design of EED Binders Allosterically Inhibiting the Epigenetic Polycomb Repressive Complex 2 (PRC2) Methyltransferase. J Med Chem 2017; 60:415-427. [DOI: 10.1021/acs.jmedchem.6b01473] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Andreas Lingel
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Martin Sendzik
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Ying Huang
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Michael D. Shultz
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - John Cantwell
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Michael P. Dillon
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Xingnian Fu
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - John Fuller
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Tobias Gabriel
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Justin Gu
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Xiangqing Jiang
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Ling Li
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Fang Liang
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Maureen McKenna
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wei Qi
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Weijun Rao
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Xijun Sheng
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Wei Shu
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - James Sutton
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Benjamin Taft
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Long Wang
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Jue Zeng
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Hailong Zhang
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Maya Zhang
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Kehao Zhao
- Novartis Institutes for BioMedical Research, 2418 Jinke Road, Shanghai 201203, China
| | - Mika Lindvall
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Dirksen E. Bussiere
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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17
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Gobeau N, Stringer R, De Buck S, Tuntland T, Faller B. Evaluation of the GastroPlus™ Advanced Compartmental and Transit (ACAT) Model in Early Discovery. Pharm Res 2016; 33:2126-39. [PMID: 27278908 DOI: 10.1007/s11095-016-1951-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/23/2016] [Indexed: 12/17/2022]
Abstract
PURPOSE The aim of this study was to evaluate the oral exposure predictions obtained early in drug discovery with a generic GastroPlus Advanced Compartmental And Transit (ACAT) model based on the in vivo intravenous blood concentration-time profile, in silico properties (lipophilicity, pKa) and in vitro high-throughput absorption-distribution-metabolism-excretion (ADME) data (as determined by PAMPA, solubility, liver microsomal stability assays). METHODS The model was applied to a total of 623 discovery molecules and their oral exposure was predicted in rats and/or dogs. The predictions of Cmax, AUClast and Tmax were compared against the observations. RESULTS The generic model proved to make predictions of oral Cmax, AUClast and Tmax within 3-fold of the observations for rats in respectively 65%, 68% and 57% of the 537 cases. For dogs, it was respectively 77%, 79% and 85% of the 124 cases. Statistically, the model was most successful at predicting oral exposure of Biopharmaceutical Classification System (BCS) class 1 compounds compared to classes 2 and 3, and was worst at predicting class 4 compounds oral exposure. CONCLUSION The generic GastroPlus ACAT model provided reasonable predictions especially for BCS class 1 compounds. For compounds of other classes, the model may be refined by obtaining more information on solubility and permeability in secondary assays. This increases confidence that such a model can be used in discovery projects to understand the parameters limiting absorption and extrapolate predictions across species. Also, when predictions disagree with the observations, the model can be updated to test hypotheses and understand oral absorption.
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Affiliation(s)
- N Gobeau
- Metabolism and Pharmacokinetics (MAP) Department, Novartis Institutes for Biomedical Research, Basel, Switzerland.
- Medicines for Malaria Venture, Route de Pré-Bois 20, PO Box 1826, 1215, Geneva 15, Switzerland.
| | - R Stringer
- Metabolism and Pharmacokinetics (MAP) Department, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - S De Buck
- Drug Metabolism and Pharmacokinetics (DMPK) Department, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - T Tuntland
- Metabolism and Pharmacokinetics (MAP) Department, Genomics Institute of the Novartis Foundation, Novartis Institutes for Biomedical Research, San Diego, California, USA
| | - B Faller
- Metabolism and Pharmacokinetics (MAP) Department, Novartis Institutes for Biomedical Research, Basel, Switzerland
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