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Moreau F, Atamanyuk D, Blaukopf M, Barath M, Herczeg M, Xavier NM, Monbrun J, Airiau E, Henryon V, Leroy F, Floquet S, Bonnard D, Szabla R, Brown C, Junop MS, Kosma P, Gerusz V. Potentiating Activity of GmhA Inhibitors on Gram-Negative Bacteria. J Med Chem 2024; 67:6610-6623. [PMID: 38598312 PMCID: PMC11056994 DOI: 10.1021/acs.jmedchem.4c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/28/2024] [Accepted: 03/29/2024] [Indexed: 04/12/2024]
Abstract
Inhibition of the biosynthesis of bacterial heptoses opens novel perspectives for antimicrobial therapies. The enzyme GmhA responsible for the first committed biosynthetic step catalyzes the conversion of sedoheptulose 7-phosphate into d-glycero-d-manno-heptose 7-phosphate and harbors a Zn2+ ion in the active site. A series of phosphoryl- and phosphonyl-substituted derivatives featuring a hydroxamate moiety were designed and prepared from suitably protected ribose or hexose derivatives. High-resolution crystal structures of GmhA complexed to two N-formyl hydroxamate inhibitors confirmed the binding interactions to a central Zn2+ ion coordination site. Some of these compounds were found to be nanomolar inhibitors of GmhA. While devoid of HepG2 cytotoxicity and antibacterial activity of their own, they demonstrated in vitro lipopolysaccharide heptosylation inhibition in Enterobacteriaceae as well as the potentiation of erythromycin and rifampicin in a wild-type Escherichia coli strain. These inhibitors pave the way for a novel treatment of Gram-negative infections.
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Affiliation(s)
- François Moreau
- Mutabilis, 102 Avenue Gaston Roussel, Romainville 93230, France
| | | | - Markus Blaukopf
- Department
of Chemistry, University of Natural Resources
and Life Sciences, Muthgasse
18, Vienna A-1190, Austria
| | - Marek Barath
- Department
of Chemistry, University of Natural Resources
and Life Sciences, Muthgasse
18, Vienna A-1190, Austria
- Institute
of Chemistry, Center for Glycomics, Slovak
Academy of Sciences, Dúbravská cesta 9, Bratislava SK-845 38, Slovakia
| | - Mihály Herczeg
- Department
of Chemistry, University of Natural Resources
and Life Sciences, Muthgasse
18, Vienna A-1190, Austria
- Department
of Pharmaceutical Chemistry, University
of Debrecen, Debrecen 4032, Hungary
| | - Nuno M. Xavier
- Department
of Chemistry, University of Natural Resources
and Life Sciences, Muthgasse
18, Vienna A-1190, Austria
- Centro
de Química Estrutural, Institute of Molecular Sciences, Faculdade de Ciências, Universidade de Lisboa, Ed. C8, 5° Piso, Campo Grande, Lisboa 1749-016, Portugal
| | | | | | | | - Frédéric Leroy
- Carbosynth
Limited, 8&9 Old
Station Business Park, Compton, Berkshire RG20 6NE, U.K.
| | | | - Damien Bonnard
- Mutabilis, 102 Avenue Gaston Roussel, Romainville 93230, France
| | - Robert Szabla
- Department
of Biochemistry, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Chris Brown
- Department
of Biochemistry, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Murray S. Junop
- Department
of Biochemistry, University of Western Ontario, London, ON N6A 3K7, Canada
| | - Paul Kosma
- Department
of Chemistry, University of Natural Resources
and Life Sciences, Muthgasse
18, Vienna A-1190, Austria
| | - Vincent Gerusz
- Mutabilis, 102 Avenue Gaston Roussel, Romainville 93230, France
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Soni M, Srivastava G, Ramalingam K, Shakya AK, Siddiqi MI, Pratap JV. Identification of potent inhibitors for Leishmania donovani homoserine kinase: an integrated in silico and kinetic study. J Biomol Struct Dyn 2023:1-16. [PMID: 37962849 DOI: 10.1080/07391102.2023.2279279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023]
Abstract
Leishmaniasis is caused by ∼20 species of Leishmania that affects millions in endemic areas. Available therapies are not sufficient to effectively control the disease, cause severe side effects and eventually lead to drug resistance, making the discovery of novel therapeutic molecules an immediate need. Molecular target-based drug discovery, where the target is a defined molecular gene, protein or a mechanism, is a rationale driven approach for novel therapeutics. Humans obtain the essential amino acid such as threonine from dietary sources, while Leishmania synthesize it de-novo. Enzymes of the threonine biosynthesis pathway, including the rate limiting Homoserine kinase (HSK) which converts L-homoserine into ortho-phospho homoserine are thus attractive targets for rationale driven therapy. The absence of HSK in humans and its presence in Leishmania donovani enhances the opportunity to exploit HSK as a molecular target for anti-leishmanials therapeutic development. In this study, we utilize structure-based high throughput drug discovery (SBDD), followed by biochemical validation and identified two potential inhibitors (RH00038 and S02587) from Maybridge chemical library that targets L. donovani HSK. These two inhibitors effectively induced the mortality of Leishmania donovani in both amastigote and promastigote stages, with one of them being specific to parasite and twice as effective as the standard therapeutic molecule.
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Affiliation(s)
- Mohini Soni
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India
| | - Gaurava Srivastava
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Karthik Ramalingam
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Anil Kumar Shakya
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Imran Siddiqi
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India
| | - J Venkatesh Pratap
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India
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Yeh CW, Feng CC, Chen PL, Jhou YJ, Hou DR. Enantioselective Synthesis of Nabscessin C. J Org Chem 2023; 88:13528-13534. [PMID: 37681712 DOI: 10.1021/acs.joc.3c01064] [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: 09/09/2023]
Abstract
Enantioselective synthesis of nabscessin C (1), an aminocyclitol amide with antimicrobial activity, is reported. Starting from myo-inositol, (+)-nabscessin C was synthesized in 12 isolation steps. Desymmetrization of 2-deoxygenated 4,6-dibenzylinositol was achieved using lipase from porcine pancreas (PPL), and the stereochemistry was established by X-ray crystallography. This method has the potential for synthesizing other cyclitol-derived compounds.
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Affiliation(s)
- Chun-Wei Yeh
- Department of Chemistry, National Central University, 300 Jhong-Da Road, Jhong-Li, Taoyuan 320317, Taiwan
| | - Chia-Chi Feng
- Department of Chemistry, National Central University, 300 Jhong-Da Road, Jhong-Li, Taoyuan 320317, Taiwan
| | - Pei-Lin Chen
- Instrument Center, National Tsing Hua University, 101 Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan
| | - Yi-Jhen Jhou
- Department of Chemistry, National Central University, 300 Jhong-Da Road, Jhong-Li, Taoyuan 320317, Taiwan
| | - Duen-Ren Hou
- Department of Chemistry, National Central University, 300 Jhong-Da Road, Jhong-Li, Taoyuan 320317, Taiwan
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Kadeřábková N, Mahmood AJS, Furniss RCD, Mavridou DAI. Making a chink in their armor: Current and next-generation antimicrobial strategies against the bacterial cell envelope. Adv Microb Physiol 2023; 83:221-307. [PMID: 37507160 PMCID: PMC10517717 DOI: 10.1016/bs.ampbs.2023.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Gram-negative bacteria are uniquely equipped to defeat antibiotics. Their outermost layer, the cell envelope, is a natural permeability barrier that contains an array of resistance proteins capable of neutralizing most existing antimicrobials. As a result, its presence creates a major obstacle for the treatment of resistant infections and for the development of new antibiotics. Despite this seemingly impenetrable armor, in-depth understanding of the cell envelope, including structural, functional and systems biology insights, has promoted efforts to target it that can ultimately lead to the generation of new antibacterial therapies. In this article, we broadly overview the biology of the cell envelope and highlight attempts and successes in generating inhibitors that impair its function or biogenesis. We argue that the very structure that has hampered antibiotic discovery for decades has untapped potential for the design of novel next-generation therapeutics against bacterial pathogens.
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Affiliation(s)
- Nikol Kadeřábková
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Ayesha J S Mahmood
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - R Christopher D Furniss
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Despoina A I Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States; John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, TX, United States.
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Sengupta S, Abhinav N, Singh S, Dutta J, Mabalirajan U, Kaliyamurthy K, Mukherjee PK, Jaisankar P, Bandyopadhyay A. Standardised Sonneratia apetala Buch.-Ham. fruit extract inhibits human neutrophil elastase and attenuates elastase-induced lung injury in mice. Front Pharmacol 2022; 13:1011216. [PMID: 36569308 PMCID: PMC9768866 DOI: 10.3389/fphar.2022.1011216] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) along with asthma is a major and increasing global health problem. Smoking contributes to about 80%-90% of total COPD cases in the world. COPD leads to the narrowing of small airways and destruction of lung tissue leading to emphysema primarily caused by neutrophil elastase. Neutrophil elastase plays an important role in disease progression in COPD patients and has emerged as an important target for drug discovery. Sonneratia apetala Buch.-Ham. is a mangrove plant belonging to family Sonneratiaceae. It is widely found in the Sundarban regions of India. While the fruits of this plant have antibacterial, antifungal, antioxidant and astringent activities, fruit and leaf extracts have been shown to reduce the symptoms of asthma and cough. The aim of this study is to find whether hydro alcoholic fruit extracts of S. apetala inhibit neutrophil elastase and thus prevent the progression of neutrophil elastase-driven lung emphysema. The hydroalcoholic extract, ethanol: water (90:10), of the S. apetala Buch.-Ham. fresh fruits (SAM) were used for neutrophil elastase enzyme kinetic assay and IC50 of the extract was determined. The novel HPLC method has been developed and the extract was standardized with gallic acid and ellagic acid as standards. The extract was further subjected to LC-MS2 profiling to identify key phytochemicals. The standardized SAM extract contains 53 μg/mg of gallic acid and 95 μg/mg of ellagic acid, based on the HPLC calibration curve. SAM also reversed the elastase-induced morphological change of human epithelial cells and prevented the release of ICAM-1 in vitro and an MTT assay was conducted to assess the viability. Further, 10 mg/kg SAM had reduced alveolar collapse induced by neutrophil elastase in the mice model. Thus, in this study, we reported for the first time that S. apetala fruit extract has the potential to inhibit human neutrophil elastase in vitro and in vivo.
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Affiliation(s)
- Sayantan Sengupta
- Cardiovascular Disease and Respiratory Disorders Laboratory, Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Nipun Abhinav
- Department of Natural Products, National Institute of Pharmaceutical Education and Research (NIPER), Kolkata, India
| | - Sabita Singh
- Molecular Pathobiology of Respiratory Diseases Laboratory, Cell Biology and Physiology Department, CSIR-Indian Institute of Chemical Biology, Kolkata, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Joytri Dutta
- Molecular Pathobiology of Respiratory Diseases Laboratory, Cell Biology and Physiology Department, CSIR-Indian Institute of Chemical Biology, Kolkata, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ulaganathan Mabalirajan
- Molecular Pathobiology of Respiratory Diseases Laboratory, Cell Biology and Physiology Department, CSIR-Indian Institute of Chemical Biology, Kolkata, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Karthigeyan Kaliyamurthy
- Central National Herbarium, Botanical Survey of India, A.J.C.B. Indian Botanic Garden, Howrah, India
| | | | - Parasuraman Jaisankar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,Laboratory of Catalysis and Chemical Biology, Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, Kolkata, India,*Correspondence: Parasuraman Jaisankar, ; Arun Bandyopadhyay,
| | - Arun Bandyopadhyay
- Cardiovascular Disease and Respiratory Disorders Laboratory, Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,*Correspondence: Parasuraman Jaisankar, ; Arun Bandyopadhyay,
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Sengupta S, Reddy JR, Rajesh N, Jaiswal A, Mabalirajan U, Palakodety RK, Mukherjee P, Bandyopadhyay A. Novel benzoxazinone derivative as potent human neutrophil elastase inhibitor: Potential implications in lung injury. Eur J Pharmacol 2022; 931:175187. [PMID: 35952844 DOI: 10.1016/j.ejphar.2022.175187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/25/2022]
Abstract
Neutrophil elastase, a powerful physiological defence tool, may serve as drug target for diverse diseases due to its bystander effect on host cells like chronic obstructive pulmonary disease (COPD). Here, we synthesised seven novel benzoxazinone derivatives and identified that these synthetic compounds are human neutrophil elastase inhibitor that was demonstrated by enzyme substrate kinetic assay. One such compound, PD05, emerged as the most potent inhibitor with lower IC50 as compared to control drug sivelestat. While this inhibition is competitive based on substrate dilution assay, PD05 showed a high binding affinity for human neutrophil elastase (Kd = 1.63 nM) with faster association and dissociation rate compared to notable elastase inhibitors like ONO 6818 and AZD9668, and its interaction with human neutrophil elastase was fully reversible.Preclinical pharmacokinetic studies were performed in vitro where protein binding was found to be 72% with a high recovery rate, aqueous solubility of 194.7 μM, low permeability along with a favourable hERG. Experiments with cell line revealed that the molecule successfully prevented elastase induced rounding and retracted cell morphology and cell cytotoxicity. In mouse model PD05 is able to reduce the alveolar collapse induced by neutrophil elastase. In summary, we demonstrate the in situ, in vitro and in vivo anti-elastase potential of the newly synthesised benzoxazinone derivative PD05 and thus this could be promising candidate for further investigation as a drug for the treatment of COPD.
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Affiliation(s)
- Sayantan Sengupta
- Cardiovascular Disease & Respiratory Disorders Laboratory, Department of Cell Biology & Physiology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Jala Ranjith Reddy
- Division of Organic and Biomolecular Medicine, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Nomula Rajesh
- Division of Organic and Biomolecular Medicine, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Ashish Jaiswal
- Molecular Pathobiology of Respiratory Diseases, Department of Cell Biology & Physiology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Ulaganathan Mabalirajan
- Molecular Pathobiology of Respiratory Diseases, Department of Cell Biology & Physiology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Radha Krishna Palakodety
- Division of Organic and Biomolecular Medicine, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Pulok Mukherjee
- Institute of Bioresources and Sustainable Development (IBSD), Imphal, Manipur, India
| | - Arun Bandyopadhyay
- Cardiovascular Disease & Respiratory Disorders Laboratory, Department of Cell Biology & Physiology, CSIR-Indian Institute of Chemical Biology, Kolkata, India.
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