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Lan T, Ganapathy US, Sharma S, Ahn Y, Zimmerman M, Molodtsov V, Hegde P, Gengenbacher M, Ebright RH, Dartois V, Freundlich JS, Dick T, Aldrich CC. Redesign of Rifamycin Antibiotics to Overcome ADP-Ribosylation-Mediated Resistance. Angew Chem Int Ed Engl 2022; 61:e202211498. [PMID: 36222275 PMCID: PMC9633546 DOI: 10.1002/anie.202211498] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 11/11/2022]
Abstract
Rifamycin antibiotics are a valuable class of antimicrobials for treating infections by mycobacteria and other persistent bacteria owing to their potent bactericidal activity against replicating and non-replicating pathogens. However, the clinical utility of rifamycins against Mycobacterium abscessus is seriously compromised by a novel resistance mechanism, namely, rifamycin inactivation by ADP-ribosylation. Using a structure-based approach, we rationally redesign rifamycins through strategic modification of the ansa-chain to block ADP-ribosylation while preserving on-target activity. Validated by a combination of biochemical, structural, and microbiological studies, the most potent analogs overcome ADP-ribosylation, restored their intrinsic low nanomolar activity and demonstrated significant in vivo antibacterial efficacy. Further optimization by tuning drug disposition properties afforded a preclinical candidate with remarkable potency and an outstanding pharmacokinetic profile.
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Affiliation(s)
- Tian Lan
- Department of Medicinal ChemistryCollege of PharmacyUniversity of Minnesota308 SE Harvard St SEMinneapolisMN 55455USA
| | - Uday S. Ganapathy
- Center for Discovery and InnovationHackensack Meridian Health & Department of Medical SciencesHackensack Meridian School of Medicine123 Metro BoulevardNutleyNJ 07110USA
| | - Sachin Sharma
- Department of Medicinal ChemistryCollege of PharmacyUniversity of Minnesota308 SE Harvard St SEMinneapolisMN 55455USA
| | - Yong‐Mo Ahn
- Department of Pharmacology and PhysiologyDepartment of MedicineCenter for Emerging and Reemerging PathogensRutgers University185 South Orange AvenueNewarkNJ 07103USA,National Center for Advancing Translational SciencesNational Institutes of HealthRockvilleMD 20850USA
| | - Matthew Zimmerman
- Center for Discovery and InnovationHackensack Meridian Health & Department of Medical SciencesHackensack Meridian School of Medicine123 Metro BoulevardNutleyNJ 07110USA
| | - Vadim Molodtsov
- Waksman InstituteRutgers University190 Frelinghuysen RoadPiscatawayNJ 08854USA
| | - Pooja Hegde
- Department of Medicinal ChemistryCollege of PharmacyUniversity of Minnesota308 SE Harvard St SEMinneapolisMN 55455USA
| | - Martin Gengenbacher
- Center for Discovery and InnovationHackensack Meridian Health & Department of Medical SciencesHackensack Meridian School of Medicine123 Metro BoulevardNutleyNJ 07110USA
| | - Richard H. Ebright
- Waksman InstituteRutgers University190 Frelinghuysen RoadPiscatawayNJ 08854USA
| | - Véronique Dartois
- Center for Discovery and InnovationHackensack Meridian Health & Department of Medical SciencesHackensack Meridian School of Medicine123 Metro BoulevardNutleyNJ 07110USA
| | - Joel S. Freundlich
- Department of Pharmacology and PhysiologyDepartment of MedicineCenter for Emerging and Reemerging PathogensRutgers University185 South Orange AvenueNewarkNJ 07103USA
| | - Thomas Dick
- Center for Discovery and InnovationHackensack Meridian Health & Department of Medical SciencesHackensack Meridian School of Medicine123 Metro BoulevardNutleyNJ 07110USA,Department of Microbiology and ImmunologyGeorgetown University3900 Reservoir Road NWWashingtonDC 20007USA
| | - Courtney C. Aldrich
- Department of Medicinal ChemistryCollege of PharmacyUniversity of Minnesota308 SE Harvard St SEMinneapolisMN 55455USA
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Lan T, Ganapathy US, Sharma S, Ahn Y, Zimmerman M, Molodtsov V, Hegde P, Gengenbacher M, Ebright RH, Dartois V, Freundlich JS, Dick T, Aldrich CC. Redesign of Rifamycin Antibiotics to Overcome ADP‐Ribosylation‐Mediated Resistance. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202211498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tian Lan
- Department of Medicinal Chemistry College of Pharmacy University of Minnesota 308 SE Harvard St SE Minneapolis MN 55455 USA
| | - Uday S. Ganapathy
- Center for Discovery and Innovation Hackensack Meridian Health & Department of Medical Sciences Hackensack Meridian School of Medicine 123 Metro Boulevard Nutley NJ 07110 USA
| | - Sachin Sharma
- Department of Medicinal Chemistry College of Pharmacy University of Minnesota 308 SE Harvard St SE Minneapolis MN 55455 USA
| | - Yong‐Mo Ahn
- Department of Pharmacology and Physiology Department of Medicine Center for Emerging and Reemerging Pathogens Rutgers University 185 South Orange Avenue Newark NJ 07103 USA
- National Center for Advancing Translational Sciences National Institutes of Health Rockville MD 20850 USA
| | - Matthew Zimmerman
- Center for Discovery and Innovation Hackensack Meridian Health & Department of Medical Sciences Hackensack Meridian School of Medicine 123 Metro Boulevard Nutley NJ 07110 USA
| | - Vadim Molodtsov
- Waksman Institute Rutgers University 190 Frelinghuysen Road Piscataway NJ 08854 USA
| | - Pooja Hegde
- Department of Medicinal Chemistry College of Pharmacy University of Minnesota 308 SE Harvard St SE Minneapolis MN 55455 USA
| | - Martin Gengenbacher
- Center for Discovery and Innovation Hackensack Meridian Health & Department of Medical Sciences Hackensack Meridian School of Medicine 123 Metro Boulevard Nutley NJ 07110 USA
| | - Richard H. Ebright
- Waksman Institute Rutgers University 190 Frelinghuysen Road Piscataway NJ 08854 USA
| | - Véronique Dartois
- Center for Discovery and Innovation Hackensack Meridian Health & Department of Medical Sciences Hackensack Meridian School of Medicine 123 Metro Boulevard Nutley NJ 07110 USA
| | - Joel S. Freundlich
- Department of Pharmacology and Physiology Department of Medicine Center for Emerging and Reemerging Pathogens Rutgers University 185 South Orange Avenue Newark NJ 07103 USA
| | - Thomas Dick
- Center for Discovery and Innovation Hackensack Meridian Health & Department of Medical Sciences Hackensack Meridian School of Medicine 123 Metro Boulevard Nutley NJ 07110 USA
- Department of Microbiology and Immunology Georgetown University 3900 Reservoir Road NW Washington DC 20007 USA
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry College of Pharmacy University of Minnesota 308 SE Harvard St SE Minneapolis MN 55455 USA
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Paulowski L, Beckham KSH, Johansen MD, Berneking L, Van N, Degefu Y, Staack S, Sotomayor FV, Asar L, Rohde H, Aldridge BB, Aepfelbacher M, Parret A, Wilmanns M, Kremer L, Combrink K, Maurer FP. C25-modified rifamycin derivatives with improved activity against Mycobacterium abscessus. PNAS NEXUS 2022; 1:pgac130. [PMID: 36714853 PMCID: PMC9802118 DOI: 10.1093/pnasnexus/pgac130] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/05/2022] [Indexed: 02/01/2023]
Abstract
Infections caused by Mycobacterium abscessus are difficult to treat due to its intrinsic resistance to most antibiotics. Formation of biofilms and the capacity of M. abscessus to survive inside host phagocytes further complicate eradication. Herein, we explored whether addition of a carbamate-linked group at the C25 position of rifamycin SV blocks enzymatic inactivation by ArrMab, an ADP-ribosyltransferase conferring resistance to rifampicin (RMP). Unlike RMP, 5j, a benzyl piperidine rifamycin derivative with a morpholino substituted C3 position and a naphthoquinone core, is not modified by purified ArrMab. Additionally, we show that the ArrMab D82 residue is essential for catalytic activity. Thermal profiling of ArrMab in the presence of 5j, RMP, or rifabutin shows that 5j does not bind to ArrMab. We found that the activity of 5j is comparable to amikacin against M. abscessus planktonic cultures and pellicles. Critically, 5j also exerts potent antimicrobial activity against M. abscessus in human macrophages and shows synergistic activity with amikacin and azithromycin.
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Affiliation(s)
| | | | | | | | - Nhi Van
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, MA 02111, USA
| | - Yonatan Degefu
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, MA 02111, USA
| | - Sonja Staack
- European Molecular Biology Laboratory, 22607 Hamburg, Germany
| | - Flor Vasquez Sotomayor
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany,Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Lucia Asar
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, MA 02111, USA
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Annabel Parret
- European Molecular Biology Laboratory, 22607 Hamburg, Germany,Charles River Laboratories, 2340 Beerse, Belgium
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, 22607 Hamburg, Germany,University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 34293 Montpellier, France,INSERM, Institut de Recherche en Infectiologie de Montpellier, 34293 Montpellier, France
| | - Keith Combrink
- Department of Chemistry and Biochemistry, Texas A&M International University, Laredo, TX 77843, USA,Department of Chemistry, Blinn College, Bryan Campus, Brenham, TX 77833, USA
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Skrzypczak N, Przybylski P. Modifications, biological origin and antibacterial activity of naphthalenoid ansamycins. Nat Prod Rep 2022; 39:1653-1677. [PMID: 35244668 DOI: 10.1039/d2np00002d] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: 2011 to 2021Structural division of natural naphthalenoid ansamycins, regarding the type of the core and length of the ansa chain, and their biosynthetic pathways in microorganisms are discussed. The great biosynthetic plasticity of natural naphthalenoid ansamycins is reflected in their structural variety due to the alterations within ansa bridge or naphthalenoid core portions. A comparison between the biological potency of natural and semisynthetic naphthalenoid ansamycins was performed and discussed in relation to the molecular targets in cells. The antibacterial potency of naphthalenoid ansamycins seems to be dependent on the ansa chain length and conformational flexibility - the higher flexibility of the ansa chain the better biological outcome is noted.
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Affiliation(s)
- Natalia Skrzypczak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland.
| | - Piotr Przybylski
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland.
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Illouz M, Alcaraz M, Roquet-Banères F, Kremer L. [Mycobacterium abscessus, a model of resistance to multiple antibiotic classes]. Med Sci (Paris) 2021; 37:993-1001. [PMID: 34851275 DOI: 10.1051/medsci/2021164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mycobacterium abscessus is an environmental fast-growing, non-tuberculous mycobacterium responsible for severe lung infections, especially in patients with underlying lung disorders such as cystic fibrosis. The standard chemotherapy combines a b-lactam (imipenem or cefoxitin), an aminoglycoside (amikacin) and a macrolide (clarithromycin or azithromycin). However, resistance of this bacterium to most antibiotic classes, including nearly all anti-tubercular drugs, leads frequently to treatment failure and considerably reduces the therapeutic arsenal available to the clinician. A comprehensive understanding of the innate and acquired resistance mechanisms is thus necessary to counteract M. abscessus lung infections.
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Affiliation(s)
- Morgane Illouz
- CNRS UMR 9004, Institut de recherche en infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
| | - Matthéo Alcaraz
- CNRS UMR 9004, Institut de recherche en infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
| | - Françoise Roquet-Banères
- CNRS UMR 9004, Institut de recherche en infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
| | - Laurent Kremer
- CNRS UMR 9004, Institut de recherche en infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France - Inserm, IRIM, 34293 Montpellier, France
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Blocking Bacterial Naphthohydroquinone Oxidation and ADP-Ribosylation Improves Activity of Rifamycins against Mycobacterium abscessus. Antimicrob Agents Chemother 2021; 65:e0097821. [PMID: 34228543 PMCID: PMC8370238 DOI: 10.1128/aac.00978-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rifampicin is an effective drug for treating tuberculosis (TB) but is not used to treat Mycobacterium abscessus infections due to poor in vitro activity. While rifabutin, another rifamycin, has better anti-M. abscessus activity, its activity is far from the nanomolar potencies of rifamycins against Mycobacterium tuberculosis. Here, we asked (i) why is rifabutin more active against M. abscessus than rifampicin, and (ii) why is rifabutin's anti-M. abscessus activity poorer than its anti-TB activity? Comparative analysis of naphthoquinone- versus naphthohydroquinone-containing rifamycins suggested that the improved activity of rifabutin over rifampicin is linked to its less readily oxidizable naphthoquinone core. Although rifabutin is resistant to bacterial oxidation, metabolite and genetic analyses showed that this rifamycin is metabolized by the ADP-ribosyltransferase ArrMab like rifampicin, preventing it from achieving the nanomolar activity that it displays against M. tuberculosis. Based on the identified dual mechanism of intrinsic rifamycin resistance, we hypothesized that rifamycins more potent than rifabutin should contain the molecule's naphthoquinone core plus a modification that blocks ADP-ribosylation at its C-23. To test these predictions, we performed a blinded screen of a diverse collection of 189 rifamycins and identified two molecules more potent than rifabutin. As predicted, these compounds contained both a more oxidatively resistant naphthoquinone core and C-25 modifications that blocked ADP-ribosylation. Together, this work revealed dual bacterial metabolism as the mechanism of intrinsic resistance of M. abscessus to rifamycins and provides proof of concept for the repositioning of rifamycins for M. abscessus disease by developing derivatives that resist both bacterial oxidation and ADP-ribosylation.
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Rifabutin Is Inactivated by Mycobacterium abscessus Arr. Antimicrob Agents Chemother 2021; 65:AAC.02215-20. [PMID: 33318008 DOI: 10.1128/aac.02215-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/03/2020] [Indexed: 01/08/2023] Open
Abstract
Mycobacterium abscessus exhibits Arr (ADP-ribosyltransferase)-dependent rifampin resistance. In apparent contrast, rifabutin (RBT) has demonstrated promising activity in M. abscessus infection models, implying that RBT might not be inactivated by Arr. RBT susceptibility testing of M. abscessus Δarr revealed a strongly decreased MIC. Our findings suggest that the efficacy of RBT might be enhanced by rendering RBT resilient to Arr-dependent modification or by blocking M. abscessus Arr activity.
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Hanh BTB, Park JW, Kim TH, Kim JS, Yang CS, Jang K, Cui J, Oh DC, Jang J. Rifamycin O, An Alternative Anti- Mycobacterium abscessus Agent. Molecules 2020; 25:molecules25071597. [PMID: 32244387 PMCID: PMC7181020 DOI: 10.3390/molecules25071597] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium abscessus is the most difficult-to-treat nontuberculous mycobacteria because of its resistance to many antibiotics. In this study, we screened the Korea Chemical Bank library for a bioluminescent reporter assay to identify molecules capable of acting against M. abscessus. On application of the assay, rifamycin O showed excellent in vitro activity with a narrow range of the minimum inhibitory concentration required to inhibit the growth of 90% of the bacterium (MIC90 = 4.0-6.2 μM); its in vivo efficacy in the zebrafish (Danio rerio) infection model was comparable to that of rifabutin at 25 μM. Furthermore, rifamycin O did not show significant toxicity in cells and the zebrafish model. These results are the first in vivo indication that rifamycin O may be a drug candidate for treating M. abscessus infections.
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Affiliation(s)
- Bui Thi Bich Hanh
- Molecular Mechanisms of Antibiotics, Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea; (B.T.B.H.); (T.H.K.)
- Division of Applied Life Science (BK21plus Program), Gyeongsang National University, Jinju 52828, Korea
| | - June-Woo Park
- Environmental Biology Research Group, Korea Institute of Toxicology, Jinju 52834, Korea;
- Human and Environmental Toxicology Program, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Tae Ho Kim
- Molecular Mechanisms of Antibiotics, Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea; (B.T.B.H.); (T.H.K.)
- Division of Applied Life Science (BK21plus Program), Gyeongsang National University, Jinju 52828, Korea
| | - Jae-Sung Kim
- Department of Bionano Technology, Hanyang University, Seoul 04763, Korea; (J.-S.K.); (C.-S.Y.)
- Department of Molecular & Life Science, Hanyang University, Ansan 15588, Korea
| | - Chul-Su Yang
- Department of Bionano Technology, Hanyang University, Seoul 04763, Korea; (J.-S.K.); (C.-S.Y.)
- Department of Molecular & Life Science, Hanyang University, Ansan 15588, Korea
| | - Kiseok Jang
- Department of Pathology, Hanyang University College of Medicine, Seoul 04763, Korea;
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (D.-C.O.)
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (D.-C.O.)
| | - Jichan Jang
- Molecular Mechanisms of Antibiotics, Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea; (B.T.B.H.); (T.H.K.)
- Division of Applied Life Science (BK21plus Program), Gyeongsang National University, Jinju 52828, Korea
- Correspondence: ; Tel.: +82-(0)55-772-1368
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