2
|
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: 2.0] [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.
Collapse
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
| |
Collapse
|