1
|
Price NPJ, Jackson MA, Hartman TM, Bannantine JP, Naumann TA, Vermillion KE, Koch AA, Kennedy PD. Precursor-Directed Biosynthesis and Biological Testing of omega-Alicyclic- and neo-Branched Tunicamycin N-Acyl Variants. ACS Chem Biol 2023; 18:2267-2280. [PMID: 37788216 DOI: 10.1021/acschembio.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Tunicamycins (TUNs) are Streptomyces-derived natural products, widely used to block protein N-glycosylation in eukaryotes or cell wall biosynthesis in bacteria. Modified or synthetic TUN analogues that uncouple these activities have considerable potential as novel mode-of-action antibacterial agents. Chemically modified TUNs reported previously with attenuated activity on yeast have pinpointed eukaryotic-specific chemophores in the uridyl group and the N-acyl chain length and terminal branching pattern. A small molecule screen of fatty acid biosynthetic primers identified several novel alicyclic- and neo-branched TUN N-acyl variants, with primer incorporation at the terminal omega-acyl position. TUNs with unique 5- and 6-carbon ω-cycloalkane and ω-cycloalkene acyl chains are produced under fermentation and in yields comparable with the native TUN. The purification, structural assignments, and the comparable antimicrobial properties of 15 of these compounds are reported, greatly extending the structural diversity of this class of compounds for potential medicinal and agricultural applications.
Collapse
Affiliation(s)
- Neil P J Price
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Michael A Jackson
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Trina M Hartman
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - John P Bannantine
- USDA, Agricultural Research Service, National Animal Disease Center, 1920 Dayton Ave., Ames, Iowa 50010, United States
| | - Todd A Naumann
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Karl E Vermillion
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Renewable Product Technology Research, 1815 N. University St., Peoria, Illinois 61604, United States
| | - Aaron A Koch
- Cayman Chemical, 1180 E. Ellsworth Rd., Ann Arbor, Michigan 48108, United States
| | - Paul D Kennedy
- Cayman Chemical, 1180 E. Ellsworth Rd., Ann Arbor, Michigan 48108, United States
| |
Collapse
|
2
|
Nakaya T, Yabe M, Mashalidis EH, Sato T, Yamamoto K, Hikiji Y, Katsuyama A, Shinohara M, Minato Y, Takahashi S, Horiuchi M, Yokota SI, Lee SY, Ichikawa S. Synthesis of macrocyclic nucleoside antibacterials and their interactions with MraY. Nat Commun 2022; 13:7575. [PMID: 36539416 PMCID: PMC9768162 DOI: 10.1038/s41467-022-35227-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
The development of new antibacterial drugs with different mechanisms of action is urgently needed to address antimicrobial resistance. MraY is an essential membrane enzyme required for bacterial cell wall synthesis. Sphaerimicins are naturally occurring macrocyclic nucleoside inhibitors of MraY and are considered a promising target in antibacterial discovery. However, developing sphaerimicins as antibacterials has been challenging due to their complex macrocyclic structures. In this study, we construct their characteristic macrocyclic skeleton via two key reactions. Having then determined the structure of a sphaerimicin analogue bound to MraY, we use a structure-guided approach to design simplified sphaerimicin analogues. These analogues retain potency against MraY and exhibit potent antibacterial activity against Gram-positive bacteria, including clinically isolated drug resistant strains of S. aureus and E. faecium. Our study combines synthetic chemistry, structural biology, and microbiology to provide a platform for the development of MraY inhibitors as antibacterials against drug-resistant bacteria.
Collapse
Affiliation(s)
- Takeshi Nakaya
- grid.39158.360000 0001 2173 7691Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan
| | - Miyuki Yabe
- grid.39158.360000 0001 2173 7691Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan
| | - Ellene H. Mashalidis
- grid.26009.3d0000 0004 1936 7961Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710 USA ,grid.410513.20000 0000 8800 7493Present Address: Pfizer Global Research & Development, Eastern Point Road, Groton, CT 06340 USA
| | - Toyotaka Sato
- grid.39158.360000 0001 2173 7691Laboratory of Veterinary Hygiene, School/Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, 060-0818 Japan ,grid.39158.360000 0001 2173 7691Graduate School of Infectious Diseases, Hokkaido University, Sapporo, 060-0818 Japan
| | - Kazuki Yamamoto
- grid.39158.360000 0001 2173 7691Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan ,grid.39158.360000 0001 2173 7691Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan
| | - Yuta Hikiji
- grid.39158.360000 0001 2173 7691Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan
| | - Akira Katsuyama
- grid.39158.360000 0001 2173 7691Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan ,grid.39158.360000 0001 2173 7691Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan ,grid.39158.360000 0001 2173 7691Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Sapporo, Japan
| | - Motoko Shinohara
- grid.256115.40000 0004 1761 798XDepartment of Microbiology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192 Japan
| | - Yusuke Minato
- grid.256115.40000 0004 1761 798XDepartment of Microbiology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192 Japan
| | - Satoshi Takahashi
- grid.470107.5Division of Laboratory Medicine, Sapporo Medical University Hospital, South-1, West-16, Chuo-ku, Sapporo, 060-8543 Japan ,grid.263171.00000 0001 0691 0855Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, South-1, West-16, Chuo-ku, Sapporo, 060-8543 Japan
| | - Motohiro Horiuchi
- grid.39158.360000 0001 2173 7691Laboratory of Veterinary Hygiene, School/Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, 060-0818 Japan ,grid.39158.360000 0001 2173 7691Graduate School of Infectious Diseases, Hokkaido University, Sapporo, 060-0818 Japan
| | - Shin-ichi Yokota
- grid.263171.00000 0001 0691 0855Department of Microbiology, Sapporo Medical University School of Medicine, South-1, West-17, Chuo-ku, Sapporo, 060-8556 Japan
| | - Seok-Yong Lee
- grid.26009.3d0000 0004 1936 7961Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710 USA
| | - Satoshi Ichikawa
- grid.39158.360000 0001 2173 7691Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan ,grid.39158.360000 0001 2173 7691Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Japan ,grid.39158.360000 0001 2173 7691Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812 Sapporo, Japan
| |
Collapse
|
3
|
Bär D, Konetschny B, Kulik A, Xu H, Paccagnella D, Beller P, Ziemert N, Dickschat JS, Gust B. Origin of the 3-methylglutaryl moiety in caprazamycin biosynthesis. Microb Cell Fact 2022; 21:232. [PMID: 36335365 PMCID: PMC9636800 DOI: 10.1186/s12934-022-01955-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Background Caprazamycins are liponucleoside antibiotics showing bioactivity against Gram-positive bacteria including clinically relevant Mycobacterium tuberculosis by targeting the bacterial MraY-translocase. Their chemical structure contains a unique 3-methylglutaryl moiety which they only share with the closely related liposidomycins. Although the biosynthesis of caprazamycin is understood to some extent, the origin of 3-methylglutaryl-CoA for caprazamycin biosynthesis remains elusive. Results In this work, we demonstrate two pathways of the heterologous producer Streptomyces coelicolor M1154 capable of supplying 3-methylglutaryl-CoA: One is encoded by the caprazamycin gene cluster itself including the 3-hydroxy-3-methylglutaryl-CoA synthase Cpz5. The second pathway is part of primary metabolism of the host cell and encodes for the leucine/isovalerate utilization pathway (Liu-pathway). We could identify the liu cluster in S. coelicolor M1154 and gene deletions showed that the intermediate 3-methylglutaconyl-CoA is used for 3-methylglutaryl-CoA biosynthesis. This is the first report of this intermediate being hijacked for secondary metabolite biosynthesis. Furthermore, Cpz20 and Cpz25 from the caprazamycin gene cluster were found to be part of a common route after both individual pathways are merged together. Conclusions The unique 3-methylglutaryl moiety in caprazamycin originates both from the caprazamycin gene cluster and the leucine/isovalerate utilization pathway of the heterologous host. Our study enhanced the knowledge on the caprazamycin biosynthesis and points out the importance of primary metabolism of the host cell for biosynthesis of natural products. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01955-6.
Collapse
|
4
|
New MraY AA Inhibitors with an Aminoribosyl Uridine Structure and an Oxadiazole. Antibiotics (Basel) 2022; 11:antibiotics11091189. [PMID: 36139968 PMCID: PMC9495235 DOI: 10.3390/antibiotics11091189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/22/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
New inhibitors of the bacterial transferase MraY from Aquifex aeolicus (MraYAA), based on the aminoribosyl uridine central core of known natural MraY inhibitors, have been designed to generate interaction of their oxadiazole linker with the key amino acids (H324 or H325) of the enzyme active site, as observed for the highly potent inhibitors carbacaprazamycin, muraymycin D2 and tunicamycin. A panel of ten compounds was synthetized notably thanks to a robust microwave-activated one-step sequence for the synthesis of the oxadiazole ring that involved the O-acylation of an amidoxime and subsequent cyclization. The synthetized compounds, with various hydrophobic substituents on the oxadiazole ring, were tested against the MraYAA transferase activity. Although with poor antibacterial activity, nine out of the ten compounds revealed the inhibition of the MraYAA activity in the range of 0.8 µM to 27.5 µM.
Collapse
|
5
|
Kusaka S, Yamamoto K, Shinohara M, Minato Y, Ichikawa S. Design, synthesis and conformation-activity relationship analysis of LNA/BNA-type 5'-O-aminoribosyluridine as MraY inhibitors. Bioorg Med Chem 2022; 65:116744. [PMID: 35500521 DOI: 10.1016/j.bmc.2022.116744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 11/02/2022]
Abstract
It is important to understand and control the biologically active conformation in medicinal chemistry. Muraymycins and caprazamycins, which are strong inhibitors of MraY, are promising antibacterial agents with a novel mode of action. Focusing on a sugar puckering and a dihedral angle ϕ of the uridine moiety of these natural products, LNA/BNA-type 5'-O-aminoribosyluridine analogues, whose puckering of the ribose moiety are completely restricted to the N-type, were designed and synthesized as simplified MraY inhibitors. Their conformation-activity relationship was further investigated in details. The conformation-activity relationship analysis investigated in this study could be a general guideline for simplification and rational drug design of MraY inhibitory nucleoside natural products.
Collapse
Affiliation(s)
- Shintaro Kusaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kazuki Yamamoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Motoko Shinohara
- Department of Microbiology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Yusuke Minato
- Department of Microbiology, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
| |
Collapse
|
6
|
Ichikawa S. Bridge between Total Synthesis of Bioactive Natural Products and Development of Drug Leads. YAKUGAKU ZASSHI 2022; 142:355-363. [DOI: 10.1248/yakushi.21-00185-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
7
|
A Sub-Micromolar MraY AA Inhibitor with an Aminoribosyl Uridine Structure and a ( S, S)-Tartaric Diamide: Synthesis, Biological Evaluation and Molecular Modeling. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27061769. [PMID: 35335131 PMCID: PMC8954382 DOI: 10.3390/molecules27061769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 01/28/2023]
Abstract
New inhibitors of the bacterial tranferase MraY are described. Their structure is based on an aminoribosyl uridine scaffold, which is known to be important for the biological activity of natural MraY inhibitors. A decyl alkyl chain was introduced onto this scaffold through various linkers. The synthesized compounds were tested against the MraYAA transferase activity, and the most active compound with an original (S,S)-tartaric diamide linker inhibits MraY activity with an IC50 equal to 0.37 µM. Their antibacterial activity was also evaluated on a panel of Gram-positive and Gram-negative strains; however, the compounds showed no antibacterial activity. Docking and molecular dynamics studies revealed that this new linker established two stabilizing key interactions with N190 and H325, as observed for the highly potent inhibitors carbacaprazamycin, muraymycin D2 and tunicamycin.
Collapse
|
8
|
Abstract
This review deals with the synthesis of naturally occurring alkaloids containing partially or completely saturated pyrimidine nuclei. The interest in these compounds is associated with their structural diversity, high biological activity and toxicity. The review is divided into four parts, each of which describes a number of synthetic methodologies toward structurally different naturally occurring alkaloids containing saturated cyclic six-membered amidine, guanidine, aminal and urea (thiourea) moieties, respectively. The development of various synthetic strategies for the preparation of these compounds has remarkably increased during the past few decades. This is primarily due to the fact that some of these compounds are isolated only in limited quantities, which makes it practically impossible to study their full structural characteristics and biological activity.
Collapse
|
9
|
Okamoto K, Ishikawa A, Okawa R, Yamamoto K, Sato T, Yokota SI, Chiba K, Ichikawa S. Design, synthesis and biological evaluation of simplified analogues of MraY inhibitory natural product with rigid scaffold. Bioorg Med Chem 2022; 55:116556. [PMID: 35016115 DOI: 10.1016/j.bmc.2021.116556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/15/2022]
Abstract
Muraymycins and caprazamycins are strong inhibitors of MraY, which is responsible for peptidoglycan biosynthesis. Although they are promising antibacterial agents with a novel mode of action, their chemical structures are rather complex. This study investigated the simplification of these natural products by structure-based drug design, synthesis, and biological evaluation. We developed a simplified rigid scaffold with an arylalkyne moiety, which shows sub-micromolar MraY inhibitory activity. The scaffold is suitable for further investigating the structure-activity relationship by virtue of our synthetic strategy, where the substituent of interest is installed in the last stage of synthesis. This scaffold shows the potential for further use in optimizing MraY inhibitory and antibacterial activities.
Collapse
Affiliation(s)
- Kazuhiro Okamoto
- Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Aoi Ishikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Ryotaro Okawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Kazuki Yamamoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Toyotaka Sato
- Department of Microbiology, Sapporo Medical University, South-1, West-17, Chuo-ku, Sapporo 060-8556, Japan; Laboratory of Veterinary Hygiene, School/Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo 060-0818, Japan
| | - Shin-Ichi Yokota
- Department of Microbiology, Sapporo Medical University, South-1, West-17, Chuo-ku, Sapporo 060-8556, Japan
| | - Kazuhiro Chiba
- Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| |
Collapse
|
10
|
Oliver M, Le Corre L, Poinsot M, Corio A, Madegard L, Bosco M, Amoroso A, Joris B, Auger R, Touzé T, Bouhss A, Calvet-Vitale S, Gravier-Pelletier C. Synthesis, biological evaluation and molecular modeling of urea-containing MraY inhibitors. Org Biomol Chem 2021; 19:5844-5866. [PMID: 34115086 DOI: 10.1039/d1ob00710f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The straightforward synthesis of aminoribosyl uridines substituted by a 5'-methylene-urea is described. Their convergent synthesis involves the urea formation from various activated amides and an azidoribosyl uridine substituted at the 5' position by an aminomethyl group. This common intermediate resulted from the diastereoselective glycosylation of a phthalimido uridine derivative with a ribosyl fluoride as a ribosyl donor. The inhibition of the MraY transferase activity by the synthetized 11 urea-containing inhibitors was evaluated and 10 compounds revealed MraY inhibition with IC50 ranging from 1.9 μM to 16.7 μM. Their antibacterial activity was also evaluated on a panel of Gram-positive and Gram-negative bacteria. Four compounds exhibited a good activity against Gram-positive bacterial pathogens with MIC ranging from 8 to 32 μg mL-1, including methicillin resistant Staphylococcus aureus (MRSA) and Enterococcus faecium. Interestingly, one compound also revealed antibacterial activity against Pseudomonas aeruginosa with MIC equal to 64 μg mL-1. Docking experiments predicted two modes of positioning of the active compounds urea chain in different hydrophobic areas (HS2 and HS4) within the MraY active site from Aquifex aeolicus. However, molecular dynamics simulations showed that the urea chain adopts a binding mode similar to that observed in structural model and targets the hydrophobic area HS2.
Collapse
Affiliation(s)
- Martin Oliver
- Université de Paris, Faculté des Sciences, UMR CNRS 8601, LCBPT, F-75006 Paris, France.
| | - Laurent Le Corre
- Université de Paris, Faculté des Sciences, UMR CNRS 8601, LCBPT, F-75006 Paris, France.
| | - Mélanie Poinsot
- Université de Paris, Faculté des Sciences, UMR CNRS 8601, LCBPT, F-75006 Paris, France.
| | - Alessandra Corio
- Université de Paris, Faculté des Sciences, UMR CNRS 8601, LCBPT, F-75006 Paris, France.
| | - Léa Madegard
- Université de Paris, Faculté des Sciences, UMR CNRS 8601, LCBPT, F-75006 Paris, France.
| | - Michaël Bosco
- Université de Paris, Faculté des Sciences, UMR CNRS 8601, LCBPT, F-75006 Paris, France.
| | - Ana Amoroso
- Unité de Physiologie et Génétique Bactériennes, Centre d'Ingénierie des Protéines, Département des Sciences de la Vie, Université de Liège, Sart Tilman, B4000 Liège 1, Belgique
| | - Bernard Joris
- Unité de Physiologie et Génétique Bactériennes, Centre d'Ingénierie des Protéines, Département des Sciences de la Vie, Université de Liège, Sart Tilman, B4000 Liège 1, Belgique
| | - Rodolphe Auger
- Institute for Integrative Biology of the Cell (I2BC), CNRS, Université Paris Sud, CEA, F-91405, Orsay, France
| | - Thierry Touzé
- Institute for Integrative Biology of the Cell (I2BC), CNRS, Université Paris Sud, CEA, F-91405, Orsay, France
| | - Ahmed Bouhss
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | | | | |
Collapse
|
11
|
Kwak SH, Lim WY, Hao A, Mashalidis EH, Kwon DY, Jeong P, Kim MJ, Lee SY, Hong J. Synthesis and evaluation of cyclopentane-based muraymycin analogs targeting MraY. Eur J Med Chem 2021; 215:113272. [PMID: 33607457 DOI: 10.1016/j.ejmech.2021.113272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/21/2021] [Accepted: 02/02/2021] [Indexed: 11/27/2022]
Abstract
Antibiotic resistance is one of the most challenging global health issues and presents an urgent need for the development of new antibiotics. In this regard, phospho-MurNAc-pentapeptide translocase (MraY), an essential enzyme in the early stages of peptidoglycan biosynthesis, has emerged as a promising new antibiotic target. We recently reported the crystal structures of MraY in complex with representative members of naturally occurring nucleoside antibiotics, including muraymycin D2. However, these nucleoside antibiotics are synthetically challenging targets, which limits the scope of medicinal chemistry efforts on this class of compounds. To gain access to active muraymycin analogs with reduced structural complexity and improved synthetic tractability, we prepared and evaluated cyclopentane-based muraymycin analogs for targeting MraY. For the installation of the 1,2-syn-amino alcohol group of analogs, the diastereoselective isocyanoacetate aldol reaction was explored. The structure-activity relationship analysis of the synthesized analogs suggested that a lipophilic side chain is essential for MraY inhibition. Importantly, the analog 20 (JH-MR-23) showed antibacterial efficacy against Staphylococcus aureus. These findings provide insights into designing new muraymycin-based MraY inhibitors with improved chemical tractability.
Collapse
Affiliation(s)
- Seung-Hwa Kwak
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Won Young Lim
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Aili Hao
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, United States
| | - Ellene H Mashalidis
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, United States
| | - Do-Yeon Kwon
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Pyeonghwa Jeong
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Mi Jung Kim
- Department of Chemistry, Duke University, Durham, NC, 27708, United States
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, United States.
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC, 27708, United States.
| |
Collapse
|
12
|
Terasawa Y, Sataka C, Sato T, Yamamoto K, Fukushima Y, Nakajima C, Suzuki Y, Katsuyama A, Matsumaru T, Yakushiji F, Yokota SI, Ichikawa S. Elucidating the Structural Requirement of Uridylpeptide Antibiotics for Antibacterial Activity. J Med Chem 2020; 63:9803-9827. [PMID: 32787111 DOI: 10.1021/acs.jmedchem.0c00973] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The synthesis and biological evaluation of analogues of uridylpeptide antibiotics were described, and the molecular interaction between the 3'-hydroxy analogue of mureidomycin A (3'-hydroxymureidomycin A) and its target enzyme, phospho-MurNAc-pentapeptide transferase (MraY), was analyzed in detail. The structure-activity relationship (SAR) involving MraY inhibition suggests that the side chain at the urea-dipeptide moiety does not affect the MraY inhibition. However, the anti-Pseudomonas aeruginosa activity is in great contrast and the urea-dipeptide motif is a key contributor. It is also suggested that the nucleoside peptide permease NppA1A2BCD is responsible for the transport of 3'-hydroxymureidomycin A into the cytoplasm. A systematic SAR analysis of the urea-dipeptide moiety of 3'-hydroxymureidomycin A was further conducted and the antibacterial activity was determined. This study provides a guide for the rational design of analogues based on uridylpeptide antibiotics.
Collapse
Affiliation(s)
- Yuma Terasawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Chisato Sataka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Toyotaka Sato
- Department of Microbiology, Sapporo Medical University School of Medicine, South-1, West-17, Chuo-ku, Sapporo 060-8556, Japan
| | - Kazuki Yamamoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Yukari Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo 001-0020, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo 001-0020, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo 001-0020, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo 001-0020, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo 001-0020, Japan
| | - Akira Katsuyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.,Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Takanori Matsumaru
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.,Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Fumika Yakushiji
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.,Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Shin-Ichi Yokota
- Department of Microbiology, Sapporo Medical University School of Medicine, South-1, West-17, Chuo-ku, Sapporo 060-8556, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.,Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| |
Collapse
|
13
|
Antibacterial Activities of Selected Pure Compounds Isolated from Gut Bacteria of Animals Living in Polluted Environments. Antibiotics (Basel) 2020; 9:antibiotics9040190. [PMID: 32316471 PMCID: PMC7235713 DOI: 10.3390/antibiotics9040190] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/04/2020] [Accepted: 04/07/2020] [Indexed: 01/16/2023] Open
Abstract
Antibiotic resistance is a global threat to public health, further accelerated by the misuse of antibiotics in humans and animals. Our recent studies have shown that gut bacteria of animals living in polluted environments are a potential source of antibacterials. Gut bacteria of cockroaches, water monitor lizards and the turtle exhibited molecules such as curcumenol, docosanedioic acid, N-acyl-homoserine lactone, L-homotyrosine and Di-rhamnolipids. Using purified compounds, assays were performed to determine their antibacterial properties using serial dilution method, cytotoxic effects using lactate dehydrogenase release, and cell viability using MTT assay. The results revealed that the purified compounds exhibited significant antibacterial activities (p < 0.05) against selected Gram-negative (Pseudomonas aeruginosa) and Gram-positive bacteria (Streptococcus pyogenes) with effective MIC50 and MIC90 at µg concentrations, and with minimal effects on human cells as observed from LDH and MTT assays. These findings are significant and provide a basis for the rational development of therapeutic antibacterials. Future studies are needed to determine in vivo effects of the identified molecules together with their mode of action, which could lead to the development of novel antibacterial(s).
Collapse
|
14
|
de Ávila MB, Bitencourt-Ferreira G, de Azevedo WF. Structural Basis for Inhibition of Enoyl-[Acyl Carrier Protein] Reductase (InhA) from Mycobacterium tuberculosis. Curr Med Chem 2020; 27:745-759. [DOI: 10.2174/0929867326666181203125229] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 07/26/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022]
Abstract
Background::
The enzyme trans-enoyl-[acyl carrier protein] reductase (InhA) is a central
protein for the development of antitubercular drugs. This enzyme is the target for the pro-drug
isoniazid, which is catalyzed by the enzyme catalase-peroxidase (KatG) to become active.
Objective::
Our goal here is to review the studies on InhA, starting with general aspects and focusing on
the recent structural studies, with emphasis on the crystallographic structures of complexes involving
InhA and inhibitors.
Method::
We start with a literature review, and then we describe recent studies on InhA crystallographic
structures. We use this structural information to depict protein-ligand interactions. We also analyze the
structural basis for inhibition of InhA. Furthermore, we describe the application of computational
methods to predict binding affinity based on the crystallographic position of the ligands.
Results::
Analysis of the structures in complex with inhibitors revealed the critical residues responsible
for the specificity against InhA. Most of the intermolecular interactions involve the hydrophobic residues
with two exceptions, the residues Ser 94 and Tyr 158. Examination of the interactions has shown
that many of the key residues for inhibitor binding were found in mutations of the InhA gene in the
isoniazid-resistant Mycobacterium tuberculosis. Computational prediction of the binding affinity for
InhA has indicated a moderate uphill relationship with experimental values.
Conclusion::
Analysis of the structures involving InhA inhibitors shows that small modifications on
these molecules could modulate their inhibition, which may be used to design novel antitubercular
drugs specific for multidrug-resistant strains.
Collapse
Affiliation(s)
- Maurício Boff de Ávila
- Laboratory of Computational Systems Biology, School of Sciences - Pontifical Catholic University of Rio, Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre-RS 90619-900, Brazil
| | - Gabriela Bitencourt-Ferreira
- Laboratory of Computational Systems Biology, School of Sciences - Pontifical Catholic University of Rio, Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre-RS 90619-900, Brazil
| | - Walter Filgueira de Azevedo
- Laboratory of Computational Systems Biology, School of Sciences - Pontifical Catholic University of Rio, Grande do Sul (PUCRS), Av. Ipiranga, 6681, Porto Alegre-RS 90619-900, Brazil
| |
Collapse
|
15
|
Heib A, Niro G, Weck SC, Koppermann S, Ducho C. Muraymycin Nucleoside Antibiotics: Structure-Activity Relationship for Variations in the Nucleoside Unit. Molecules 2019; 25:molecules25010022. [PMID: 31861655 PMCID: PMC6983020 DOI: 10.3390/molecules25010022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 12/04/2022] Open
Abstract
Muraymycins are a subclass of naturally occurring nucleoside antibiotics with promising antibacterial activity. They inhibit the bacterial enzyme translocase I (MraY), a clinically yet unexploited target mediating an essential intracellular step of bacterial peptidoglycan biosynthesis. Several structurally simplified muraymycin analogues have already been synthesized for structure–activity relationship (SAR) studies. We now report on novel derivatives with unprecedented variations in the nucleoside unit. For the synthesis of these new muraymycin analogues, we employed a bipartite approach facilitating the introduction of different nucleosyl amino acid motifs. This also included thymidine- and 5-fluorouridine-derived nucleoside core structures. Using an in vitro assay for MraY activity, it was found that the introduction of substituents in the 5-position of the pyrimidine nucleobase led to a significant loss of inhibitory activity towards MraY. The loss of nucleobase aromaticity (by reduction of the uracil C5-C6 double bond) resulted in a ca. tenfold decrease in inhibitory potency. In contrast, removal of the 2′-hydroxy group furnished retained activity, thus demonstrating that modifications of the ribose moiety might be well-tolerated. Overall, these new SAR insights will guide the future design of novel muraymycin analogues for their potential development towards antibacterial drug candidates.
Collapse
|
16
|
Leyerer K, Koppermann S, Ducho C. Solid Phase‐Supported Synthesis of Muraymycin Analogues. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kristin Leyerer
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Stefan Koppermann
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| | - Christian Ducho
- Department of Pharmacy Pharmaceutical and Medicinal Chemistry Saarland University Campus C2 3 66123 Saarbrücken Germany
| |
Collapse
|
17
|
Mashalidis EH, Kaeser B, Terasawa Y, Katsuyama A, Kwon DY, Lee K, Hong J, Ichikawa S, Lee SY. Chemical logic of MraY inhibition by antibacterial nucleoside natural products. Nat Commun 2019; 10:2917. [PMID: 31266949 PMCID: PMC6606608 DOI: 10.1038/s41467-019-10957-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/06/2019] [Indexed: 01/01/2023] Open
Abstract
Novel antibacterial agents are needed to address the emergence of global antibiotic resistance. MraY is a promising candidate for antibiotic development because it is the target of five classes of naturally occurring nucleoside inhibitors with potent antibacterial activity. Although these natural products share a common uridine moiety, their core structures vary substantially and they exhibit different activity profiles. An incomplete understanding of the structural and mechanistic basis of MraY inhibition has hindered the translation of these compounds to the clinic. Here we present crystal structures of MraY in complex with representative members of the liposidomycin/caprazamycin, capuramycin, and mureidomycin classes of nucleoside inhibitors. Our structures reveal cryptic druggable hot spots in the shallow inhibitor binding site of MraY that were not previously appreciated. Structural analyses of nucleoside inhibitor binding provide insights into the chemical logic of MraY inhibition, which can guide novel approaches to MraY-targeted antibiotic design.
Collapse
Affiliation(s)
- Ellene H Mashalidis
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA
| | - Benjamin Kaeser
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA
| | - Yuma Terasawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nihi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Akira Katsuyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nihi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Do-Yeon Kwon
- Department of Chemistry, Duke University, Durham, NC, 27708, USA
| | - Kiyoun Lee
- Department of Chemistry, The Catholic University of Korea, Bucheon, 14662, Korea
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC, 27708, USA
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nihi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, 303 Research Drive, Durham, NC, 27710, USA.
| |
Collapse
|
18
|
Fritillariae Thunbergii Bulbus: Traditional Uses, Phytochemistry, Pharmacodynamics, Pharmacokinetics and Toxicity. Int J Mol Sci 2019; 20:ijms20071667. [PMID: 30987173 PMCID: PMC6479889 DOI: 10.3390/ijms20071667] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 03/28/2019] [Accepted: 03/30/2019] [Indexed: 12/19/2022] Open
Abstract
Fritillariae Thunbergii Bulbus (FTB) has been widely used as an antitussive herb for thousands of years in China. However, FTB's traditional uses, chemical compounds and pharmacological activities have not been systematically reviewed. This study aimed to review its traditional uses, phytochemistry, pharmacodynamics, pharmacokinetics and toxicity. We searched the Encyclopedia of Traditional Chinese Medicine to explore the historical records which indicate that it acts to clear heat, resolve phlegm, relieve cough, remove toxicity and disperse abscesses and nodules. We searched 11 databases to identify potential phytochemical or pharmacological studies. Characteristics of its chemical constituents, pharmacological effects, pharmacokinetic and toxicity were descriptively summarized. A total of 9706 studies were identified and 83 of them were included. As a result, 134 chemical constituents were identified, including 26 alkaloids, 29 compounds found in essential oils, 13 diterpenoids, two carbohydrates, two sterols, 18 amino acids, six nucleosides, four nucleobases, four fatty acids, three lignans, and 27 elements. Thirteen pharmacological effects of FTB were identified, including anti-cancer, tracheobronchial relaxation, antitussive, expectorant, anti-muscarinic, anti-inflammation, anti-thyroid, regulation of blood rheology, antiulcer, anti-diarrhea, pain suppression, antioxidation and neuroprotection. These pharmacological activities may be mainly attributed to the alkaloids in FTB. Further phytochemical, pharmacological and network pharmacological studies are recommended.
Collapse
|
19
|
Belete TM. Novel targets to develop new antibacterial agents and novel alternatives to antibacterial agents. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.humic.2019.01.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
20
|
Linder R, Ducho C. Unified Synthesis of Densely Functionalized Amino Acid Building Blocks for the Preparation of Caprazamycin Nucleoside Antibiotics. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801667] [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)
- Ruth Linder
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| |
Collapse
|
21
|
Wiegmann D, Koppermann S, Ducho C. Aminoribosylated Analogues of Muraymycin Nucleoside Antibiotics. Molecules 2018; 23:molecules23123085. [PMID: 30486316 PMCID: PMC6320880 DOI: 10.3390/molecules23123085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 01/15/2023] Open
Abstract
Nucleoside antibiotics are uridine-derived natural products that inhibit the bacterial membrane protein MraY. MraY is a key enzyme in the membrane-associated intracellular stages of peptidoglycan biosynthesis and therefore considered to be a promising, yet unexploited target for novel antibacterial agents. Muraymycins are one subclass of such naturally occurring MraY inhibitors. As part of structure-activity relationship (SAR) studies on muraymycins and their analogues, we now report on novel derivatives with different attachment of one characteristic structural motif, i.e., the aminoribose moiety normally linked to the muraymycin glycyluridine core unit. Based on considerations derived from an X-ray co-crystal structure, we designed and synthesised muraymycin analogues having the aminoribose attached (via a linker) to either the glycyluridine amino group or to the uracil nucleobase. Reference compounds bearing the non-aminoribosylated linker units were also prepared. It was found that the novel aminoribosylated analogues were inactive as MraY inhibitors in vitro, but that the glycyluridine-modified reference compound retained most of the inhibitory potency relative to the unmodified parent muraymycin analogue. These results point to 6′-N-alkylated muraymycin analogues as a potential novel variation of the muraymycin scaffold for future SAR optimisation.
Collapse
Affiliation(s)
- Daniel Wiegmann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.
| | - Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany.
| |
Collapse
|
22
|
Analogues of Muraymycin Nucleoside Antibiotics with Epimeric Uridine-Derived Core Structures. Molecules 2018; 23:molecules23112868. [PMID: 30400295 PMCID: PMC6278576 DOI: 10.3390/molecules23112868] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/28/2018] [Accepted: 10/30/2018] [Indexed: 11/17/2022] Open
Abstract
Nucleoside analogues have found widespread application as antiviral and antitumor agents, but not yet as antibacterials. Naturally occurring uridine-derived ‘nucleoside antibiotics’ target the bacterial membrane protein MraY, an enzyme involved in peptidoglycan biosynthesis and a promising target for the development of novel antibacterial agents. Muraymycins represent a nucleoside-peptide subgroup of such MraY-inhibiting natural products. As part of detailed structure-activity relationship (SAR) studies on muraymycins and their analogues, we now report novel insights into the effects of stereochemical variations in the nucleoside core structure. Using a simplified version of the muraymycin scaffold, it was shown that some formal inversions of stereochemistry led to about one order of magnitude loss in inhibitory potency towards the target enzyme MraY. In contrast, epimers of the core motif with retained inhibitory activity were also identified. These 5′,6′-anti-configured analogues might serve as novel chemically tractable variations of the muraymycin scaffold for the future development of uridine-derived drug candidates.
Collapse
|
23
|
Hering J, Dunevall E, Ek M, Brändén G. Structural basis for selective inhibition of antibacterial target MraY, a membrane-bound enzyme involved in peptidoglycan synthesis. Drug Discov Today 2018; 23:1426-1435. [DOI: 10.1016/j.drudis.2018.05.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/13/2018] [Accepted: 05/14/2018] [Indexed: 12/16/2022]
|
24
|
Meng M, Ducho C. Oligonucleotide analogues with cationic backbone linkages. Beilstein J Org Chem 2018; 14:1293-1308. [PMID: 29977397 PMCID: PMC6009206 DOI: 10.3762/bjoc.14.111] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/26/2018] [Indexed: 12/28/2022] Open
Abstract
Their unique ability to selectively bind specific nucleic acid sequences makes oligonucleotides promising bioactive agents. However, modifications of the nucleic acid structure are an essential prerequisite for their application in vivo or even in cellulo. The oligoanionic backbone structure of oligonucleotides mainly hampers their ability to penetrate biological barriers such as cellular membranes. Hence, particular attention has been given to structural modifications of oligonucleotides which reduce their overall number of negative charges. One such approach is the site-specific replacement of the negatively charged phosphate diester linkage with alternative structural motifs which are positively charged at physiological pH, thus resulting in zwitterionic or even oligocationic backbone structures. This review provides a general overview of this concept and summarizes research on four according artificial backbone linkages: aminoalkylated phosphoramidates (and related systems), guanidinium groups, S-methylthiourea motifs, and nucleosyl amino acid (NAA)-derived modifications. The synthesis and properties of the corresponding oligonucleotide analogues are described.
Collapse
Affiliation(s)
- Melissa Meng
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| |
Collapse
|
25
|
Lukose V, Walvoort MTC, Imperiali B. Bacterial phosphoglycosyl transferases: initiators of glycan biosynthesis at the membrane interface. Glycobiology 2018; 27:820-833. [PMID: 28810664 DOI: 10.1093/glycob/cwx064] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 07/13/2017] [Indexed: 12/18/2022] Open
Abstract
Phosphoglycosyl transferases (PGTs) initiate the biosynthesis of both essential and virulence-associated bacterial glycoconjugates including lipopolysaccharide, peptidoglycan and glycoproteins. PGTs catalyze the transfer of a phosphosugar moiety from a nucleoside diphosphate sugar to a polyprenol phosphate, to form a membrane-bound polyprenol diphosphosugar product. PGTs are integral membrane proteins, which include between 1 and 11 predicted transmembrane domains. Despite this variation, common motifs have been identified in PGT families through bioinformatics and mutagenesis studies. Bacterial PGTs represent important antibacterial and virulence targets due to their significant role in initiating the biosynthesis of key bacterial glycoconjugates. Considerable effort has gone into mechanistic and inhibition studies for this class of enzymes, both of which depend on reliable, high-throughput assays for easy quantification of activity. This review summarizes recent advances made in the characterization of this challenging but important class of enzymes.
Collapse
Affiliation(s)
- Vinita Lukose
- Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Marthe T C Walvoort
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Barbara Imperiali
- Departments of Chemistry and Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
26
|
Koppermann S, Cui Z, Fischer PD, Wang X, Ludwig J, Thorson JS, Van Lanen SG, Ducho C. Insights into the Target Interaction of Naturally Occurring Muraymycin Nucleoside Antibiotics. ChemMedChem 2018; 13:779-784. [PMID: 29438582 PMCID: PMC6019934 DOI: 10.1002/cmdc.201700793] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/02/2018] [Indexed: 11/08/2022]
Abstract
Muraymycins are a subclass of antimicrobially active uridine-derived natural products. Biological data on several muraymycin analogues have been reported, including some inhibitory in vitro activities toward their target protein, the bacterial membrane enzyme MraY. However, a structure-activity relationship (SAR) study on naturally occurring muraymycins based on such in vitro data has been missing so far. In this work, we report a detailed SAR investigation on representatives of the four muraymycin subgroups A-D using a fluorescence-based in vitro MraY assay. For some muraymycins, inhibition of MraY with IC50 values in the low-picomolar range was observed. These inhibitory potencies were compared with antibacterial activities and were correlated to modelling data derived from a previously reported X-ray crystal structure of MraY in complex with a muraymycin inhibitor. Overall, these results will pave the way for the development of muraymycin analogues with optimized properties as antibacterial drug candidates.
Collapse
Affiliation(s)
- Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Zheng Cui
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
| | - Patrick D Fischer
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Xiachang Wang
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, P.R. China
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
| | - Jannine Ludwig
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone Street, Lexington, KY, 40536, USA
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany
| |
Collapse
|
27
|
N-Acetylglucosamine-1-Phosphate Transferase, WecA, as a Validated Drug Target in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2017; 61:AAC.01310-17. [PMID: 28874370 DOI: 10.1128/aac.01310-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 08/25/2017] [Indexed: 12/24/2022] Open
Abstract
The mycobacterial phosphoglycosyltransferase WecA, which initiates arabinogalactan biosynthesis in Mycobacterium tuberculosis, has been proposed as a target of the caprazamycin derivative CPZEN-45, a preclinical drug candidate for the treatment of tuberculosis. In this report, we describe the functional characterization of mycobacterial WecA and confirm the essentiality of its encoding gene in M. tuberculosis by demonstrating that the transcriptional silencing of wecA is bactericidal in vitro and in macrophages. Silencing wecA also conferred hypersensitivity of M. tuberculosis to the drug tunicamycin, confirming its target selectivity for WecA in whole cells. Simple radiometric assays performed with mycobacterial membranes and commercially available substrates allowed chemical validation of other putative WecA inhibitors and resolved their selectivity toward WecA versus another attractive cell wall target, translocase I, which catalyzes the first membrane step in the biosynthesis of peptidoglycan. These assays and the mutant strain described herein will be useful for identifying potential antitubercular leads by screening chemical libraries for novel WecA inhibitors.
Collapse
|
28
|
Ben Othman R, Fer MJ, Le Corre L, Calvet-Vitale S, Gravier-Pelletier C. Effect of uridine protecting groups on the diastereoselectivity of uridine-derived aldehyde 5'-alkynylation. Beilstein J Org Chem 2017; 13:1533-1541. [PMID: 28845198 PMCID: PMC5550804 DOI: 10.3762/bjoc.13.153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/20/2017] [Indexed: 12/17/2022] Open
Abstract
The 5'-alkynylation of uridine-derived aldehydes is described. The addition of alkynyl Grignard reagents on the carbonyl group is significantly influenced by the 2',3'-di-O-protecting groups (R1): O-alkyl groups led to modest diastereoselectivities (65:35) in favor of the 5'R-isomer, whereas O-silyl groups promoted higher diastereoselectivities (up to 99:1) in favor of the 5'S-isomer. A study related to this protecting group effect on the diastereoselectivity is reported.
Collapse
Affiliation(s)
- Raja Ben Othman
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité (USPC), Centre Interdisciplinaire Chimie Biologie-Paris (CICB-Paris), 45 rue des Saints Pères, 75270 Paris 06, France
| | - Mickaël J Fer
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité (USPC), Centre Interdisciplinaire Chimie Biologie-Paris (CICB-Paris), 45 rue des Saints Pères, 75270 Paris 06, France
| | - Laurent Le Corre
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité (USPC), Centre Interdisciplinaire Chimie Biologie-Paris (CICB-Paris), 45 rue des Saints Pères, 75270 Paris 06, France
| | - Sandrine Calvet-Vitale
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité (USPC), Centre Interdisciplinaire Chimie Biologie-Paris (CICB-Paris), 45 rue des Saints Pères, 75270 Paris 06, France
| | - Christine Gravier-Pelletier
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité (USPC), Centre Interdisciplinaire Chimie Biologie-Paris (CICB-Paris), 45 rue des Saints Pères, 75270 Paris 06, France
| |
Collapse
|
29
|
Sansanmycin natural product analogues as potent and selective anti-mycobacterials that inhibit lipid I biosynthesis. Nat Commun 2017; 8:14414. [PMID: 28248311 PMCID: PMC5337940 DOI: 10.1038/ncomms14414] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 12/21/2016] [Indexed: 12/17/2022] Open
Abstract
Tuberculosis (TB) is responsible for enormous global morbidity and mortality, and current treatment regimens rely on the use of drugs that have been in use for more than 40 years. Owing to widespread resistance to these therapies, new drugs are desperately needed to control the TB disease burden. Herein, we describe the rapid synthesis of analogues of the sansanmycin uridylpeptide natural products that represent promising new TB drug leads. The compounds exhibit potent and selective inhibition of Mycobacterium tuberculosis, the etiological agent of TB, both in vitro and intracellularly. The natural product analogues are nanomolar inhibitors of Mtb phospho-MurNAc-pentapeptide translocase, the enzyme responsible for the synthesis of lipid I in mycobacteria. This work lays the foundation for the development of uridylpeptide natural product analogues as new TB drug candidates that operate through the inhibition of peptidoglycan biosynthesis. Drug resistant tuberculosis (TB) infections are emerging at a high rate, with only few therapeutic options currently available. Here, the authors report synthetic analogues of the natural product sansanmycin that target mycobacterial cell wall biosynthesis and represent potent leads for improved anti-TB treatments.
Collapse
|
30
|
Wohnig S, Spork AP, Koppermann S, Mieskes G, Gisch N, Jahn R, Ducho C. Total Synthesis of Dansylated Park's Nucleotide for High-Throughput MraY Assays. Chemistry 2016; 22:17813-17819. [PMID: 27791327 DOI: 10.1002/chem.201604279] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Indexed: 11/11/2022]
Abstract
The membrane protein translocase I (MraY) is a key enzyme in bacterial peptidoglycan biosynthesis. It is therefore frequently discussed as a target for the development of novel antibiotics. The screening of compound libraries for the identification of MraY inhibitors is enabled by an established fluorescence-based MraY assay. However, this assay requires a dansylated derivative of the bacterial biosynthetic intermediate Park's nucleotide as the MraY substrate. Isolation of Park's nucleotide from bacteria and subsequent dansylation only furnishes limited amounts of this substrate, thus hampering the high-throughput screening for MraY inhibitors. Accordingly, the efficient provision of dansylated Park's nucleotide is a major bottleneck in the exploration of this promising drug target. In this work, we present the first total synthesis of dansylated Park's nucleotide, affording an unprecedented amount of the target compound for high-throughput MraY assays.
Collapse
Affiliation(s)
- Stephanie Wohnig
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| | - Anatol P Spork
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany.,Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| | - Gottfried Mieskes
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 1-40, 23845, Borstel, Germany
| | - Reinhard Jahn
- Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123, Saarbrücken, Germany.,Department of Chemistry, Institute of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstr. 2, 37077, Göttingen, Germany
| |
Collapse
|
31
|
Koppermann S, Ducho C. Natural Products at Work: Structural Insights into Inhibition of the Bacterial Membrane Protein MraY. Angew Chem Int Ed Engl 2016; 55:11722-4. [DOI: 10.1002/anie.201606396] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2 3 66123 Saarbrücken Germany
| |
Collapse
|
32
|
Koppermann S, Ducho C. Naturstoffe bei der Arbeit: strukturelle Einblicke in die Inhibition des bakteriellen Membranproteins MraY. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Stefan Koppermann
- Fachrichtung Pharmazie, Pharmazeutische und Medizinische, Chemie; Universität des Saarlandes; Campus C2 3 66123 Saarbrücken Deutschland
| | - Christian Ducho
- Fachrichtung Pharmazie, Pharmazeutische und Medizinische, Chemie; Universität des Saarlandes; Campus C2 3 66123 Saarbrücken Deutschland
| |
Collapse
|
33
|
Wiegmann D, Koppermann S, Wirth M, Niro G, Leyerer K, Ducho C. Muraymycin nucleoside-peptide antibiotics: uridine-derived natural products as lead structures for the development of novel antibacterial agents. Beilstein J Org Chem 2016; 12:769-795. [PMID: 27340469 PMCID: PMC4902027 DOI: 10.3762/bjoc.12.77] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/24/2016] [Indexed: 11/23/2022] Open
Abstract
Muraymycins are a promising class of antimicrobial natural products. These uridine-derived nucleoside-peptide antibiotics inhibit the bacterial membrane protein translocase I (MraY), a key enzyme in the intracellular part of peptidoglycan biosynthesis. This review describes the structures of naturally occurring muraymycins, their mode of action, synthetic access to muraymycins and their analogues, some structure-activity relationship (SAR) studies and first insights into muraymycin biosynthesis. It therefore provides an overview on the current state of research, as well as an outlook on possible future developments in this field.
Collapse
Affiliation(s)
- Daniel Wiegmann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Stefan Koppermann
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Marius Wirth
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Giuliana Niro
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Kristin Leyerer
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2 3, 66123 Saarbruecken, Germany
| |
Collapse
|