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Anti-Tuberculosis Mur Inhibitors: Structural Insights and the Way Ahead for Development of Novel Agents. Pharmaceuticals (Basel) 2023; 16:ph16030377. [PMID: 36986477 PMCID: PMC10058398 DOI: 10.3390/ph16030377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Mur enzymes serve as critical molecular devices for the synthesis of UDP-MurNAc-pentapeptide, the main building block of bacterial peptidoglycan polymer. These enzymes have been extensively studied for bacterial pathogens such as Escherichia coli and Staphylococcus aureus. Various selective and mixed Mur inhibitors have been designed and synthesized in the past few years. However, this class of enzymes remains relatively unexplored for Mycobacterium tuberculosis (Mtb), and thus offers a promising approach for drug design to overcome the challenges of battling this global pandemic. This review aims to explore the potential of Mur enzymes of Mtb by systematically scrutinizing the structural aspects of various reported bacterial inhibitors and implications concerning their activity. Diverse chemical scaffolds such as thiazolidinones, pyrazole, thiazole, etc., as well as natural compounds and repurposed compounds, have been reviewed to understand their in silico interactions with the receptor or their enzyme inhibition potential. The structural diversity and wide array of substituents indicate the scope of the research into developing varied analogs and providing valuable information for the purpose of modifying reported inhibitors of other multidrug-resistant microorganisms. Therefore, this provides an opportunity to expand the arsenal against Mtb and overcome multidrug-resistant tuberculosis.
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Elrufaie HA, Mohamed LM, Hamd AY, Bala NA, Elbadawi FA, Ghaboosh H, Alzain AA. Discovery of novel natural products as rhodesain inhibitors for human African trypanosomiasis using in silico techniques. J Biomol Struct Dyn 2022:1-13. [PMID: 35751127 DOI: 10.1080/07391102.2022.2092550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Human African Trypanosomiasis (HAT) or sleeping sickness is caused by the Trypanosoma brucei rhodesiense, a subspecies of the Trypanosomatide family. The parasite is associated with high morbidity and mortality rate in both animals and humans, claimed to be more fatal than other vector-transmitted diseases such as malaria. The majority of existing medications are highly toxic, not effective in the late chronic phase of the disease, and require maximum dosages to fully eradicate the parasite. In this study, we used computational methods to find out natural products that inhibit the Rhodesain, a parasitic enzyme that plays an important role in the parasite's pathogenicity, multiplication, and ability to pass through the host's blood-brain barrier. A library of 270540 natural products from ZINC databases was processed by using e-pharmacophore hypnosis and screening procedures, molecular docking, ADMET processes, and MM-GBSA calculations. This led to the identification of 3 compounds (ZINC000096269390, ZINC000035485292, and ZINC000035485242) which were then subjected to molecular dynamics. The findings of this study showed excellent binding affinity and stability toward the Rhodesain and suggest they may be a hopeful treatment for HAT in the future if further clinical trials were performed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hisham A Elrufaie
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Linda M Mohamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Aya Y Hamd
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Noor A Bala
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | | | - Hiba Ghaboosh
- Department of Pharmaceutics, University of Gezira, Wad Madani, Sudan
| | - Abdulrahim A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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Hrast M, Frlan R, Knez D, Zdovc I, Barreteau H, Gobec S. Mur ligases inhibitors with azastilbene scaffold: Expanding the structure-activity relationship. Bioorg Med Chem Lett 2021; 40:127966. [PMID: 33744441 DOI: 10.1016/j.bmcl.2021.127966] [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: 01/15/2021] [Revised: 03/06/2021] [Accepted: 03/10/2021] [Indexed: 11/28/2022]
Abstract
Antibiotic resistance represents one of the biggest public health challenges in the last few years. Mur ligases (MurC-MurF) are involved in the synthesis of UDP-N-acetylmuramyl-pentapeptide, the main building block of bacterial peptidoglycan polymer. They are essential for the survival of bacteria and therefore important antibacterial targets. We report herein the synthesis and structure-activity relationships of Mur ligases inhibitors with an azastilbene scaffold. Several compounds showed promising inhibitory potencies against multiple ligases and one compound also possessed moderate antibacterial activity. These results represent a solid ground for further development and optimization of structurally novel antimicrobial agents to combat the rising bacterial resistance.
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Affiliation(s)
- Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia.
| | - Rok Frlan
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Damijan Knez
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Irena Zdovc
- Veterinary Faculty, University of Ljubljana, Gerbičeva ulica 60, SI-1000 Ljubljana, Slovenia
| | - Hélène Barreteau
- Bacterial Cell Envelopes and Antibiotics Group, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia.
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Mazur G, Skiba-Kurek I, Karczewska E, Pańczyk-Straszak K, Jaworska J, Waszkielewicz AM. Design, synthesis and activity against Staphylococcus epidermidis of 5-chloro-2- or 5-chloro-4-methyl-9H-xanthen-9-one and some of its derivatives. Chem Biol Drug Des 2020; 97:674-685. [PMID: 33031630 DOI: 10.1111/cbdd.13803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/26/2020] [Indexed: 11/30/2022]
Abstract
Ten new xanthone derivatives have been designed and synthesized for their potential antibacterial activity. All compounds have been screened against Staphylococcus epidermidis strains ATCC 12228 and clinical K/12/8915. The highest antibacterial activity was observed for compound 3: 5-chloro-2-((4-(2-hydroxyethyl)piperazin-1-yl)methyl)-9H-xanthen-9-one dihydrochloride, exhibiting MIC of 0.8 µg/ml against ATCC 12228 strain, compared to linezolid (0.8 µg/ml), ciprofloxacin (0.2 µg/ml) or trimethoprim and sulfamethoxazole (0.8 µg/ml). For the most active compound 3, genotoxicity assay with use of Salmonella enterica serovar Typhimurium revealed safety in terms of genotoxicity at concentration 75 µg/ml and antibacterial activity against Salmonella at all higher concentrations. A final in silico prediction of skin metabolism of compound 3 seems promising, indicating stability of the xanthone moiety in the metabolism process.
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Affiliation(s)
- Gabriela Mazur
- Department of Bioorganic Chemistry, Chair of Organic Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
| | - Iwona Skiba-Kurek
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
| | - Elżbieta Karczewska
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Pańczyk-Straszak
- Department of Bioorganic Chemistry, Chair of Organic Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
| | - Joanna Jaworska
- Department of Bioorganic Chemistry, Chair of Organic Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
| | - Anna M Waszkielewicz
- Department of Bioorganic Chemistry, Chair of Organic Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
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5
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MurE inhibitors as antibacterial agents: a review. J INCL PHENOM MACRO 2020. [DOI: 10.1007/s10847-020-01018-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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6
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Azam MA, Jupudi S. MurD inhibitors as antibacterial agents: a review. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-020-01057-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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7
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Eniyan K, Rani J, Ramachandran S, Bhat R, Khan IA, Bajpai U. Screening of Antitubercular Compound Library Identifies Inhibitors of Mur Enzymes in Mycobacterium tuberculosis. SLAS DISCOVERY 2019; 25:70-78. [PMID: 31597510 DOI: 10.1177/2472555219881148] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The rapid rise in the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains of Mycobacterium tuberculosis (Mtb) mandates the discovery of novel tuberculosis (TB) drugs. Mur enzymes, which are identified as essential proteins in Mtb and catalyze the cytoplasmic steps in the peptidoglycan biosynthetic pathway, are considered potential drug targets. However, none of the clinical drugs have yet been developed against these enzymes. Hence, the aim of this study was to identify novel inhibitors of Mur enzymes in Mycobacterium tuberculosis. We screened an antitubercular compound library of 684 compounds, using MurB and MurE enzymes of the Mtb Mur pathway as drug targets. For experimental validation, the top hits obtained on in silico screening were screened in vitro, using Mtb Mur enzyme-specific assays. In all, seven compounds were found to show greater than 50% inhibition, with the highest inhibition observed at 77%, and the IC50 for these compounds was found to be in the range of 28-50 μM. Compound 5175112 showed the lowest IC50 (28.69 ± 1.17 μM), and on the basis of (1) the binding affinity, (2) the stability of interaction noted on molecular dynamics simulation, and (3) an in vitro assay, MurE appeared to be its target enzyme. We believe that the overall strategy followed in this study and the results obtained are a good starting point for developing Mur enzyme-specific Mtb inhibitors.
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Affiliation(s)
- Kandasamy Eniyan
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Jyoti Rani
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India.,Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Srinivasan Ramachandran
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Rahul Bhat
- Clinical Microbiology Division, Council of Scientific and Industrial Research-Indian Institute of Integrative Medicine (CSIR-IIIM), Jammu, India
| | - Inshad Ali Khan
- Clinical Microbiology Division, Council of Scientific and Industrial Research-Indian Institute of Integrative Medicine (CSIR-IIIM), Jammu, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India
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9
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Deng Y, Tang D, Wang QR, Huang S, Fu LZ, Li CH. Semi-synthesis, antibacterial activity, and molecular docking study of novel pleuromutilin derivatives bearing cinnamic acids moieties. Arch Pharm (Weinheim) 2019; 352:e1800266. [PMID: 30536467 DOI: 10.1002/ardp.201800266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/01/2018] [Accepted: 11/04/2018] [Indexed: 11/12/2022]
Abstract
To develop new antibiotics owning a special mechanism, we used the molecular assembly method to synthesize a series of novel pleuromutilin derivatives containing a cinnamic acid scaffold at the C-14 side chain. We evaluated their antibacterial activity and used in silico molecular docking to study their binding mode with the target. The structure-activity relationship (SAR) study suggested that compounds with NO2 (13e), OH (13u), and NH2 (13y) appeared more active (0.0625-2 µg/mL) in vitro against several penicillin-resistant Gram-positive bacteria and the position of the substituent on the benzene ring would affect the activity. The in vivo efficacy investigation of 13e, 13u, and 13y with once daily intragastric (i.g.) administration at 40 mg/kg for 3 consecutive days in a mouse systemic infection model showed that 13u had equal activity as valnemulin providing the mice with 60% survival, while 13e and 13y gave 30 and 40% survival, respectively. The molecular docking studies indicated that π-π stacking and hydrogen bond formation played important roles in improving the antibacterial activity.
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Affiliation(s)
- Yu Deng
- Institute of Veterinary Sciences and Pharmaceuticals, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Da Tang
- Institute of Veterinary Sciences and Pharmaceuticals, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Qiu-Ru Wang
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Sheng Huang
- Institute of Veterinary Sciences and Pharmaceuticals, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Li-Zhi Fu
- Institute of Veterinary Sciences and Pharmaceuticals, Chongqing Academy of Animal Sciences, Rongchang, China
| | - Cheng-Hong Li
- Institute of Veterinary Sciences and Pharmaceuticals, Chongqing Academy of Animal Sciences, Rongchang, China
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10
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Synthesis, molecular docking and comparative efficacy of various alkyl/aryl thioureas as antibacterial, antifungal and α-amylase inhibitors. Comput Biol Chem 2018; 77:193-198. [DOI: 10.1016/j.compbiolchem.2018.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 07/09/2018] [Accepted: 10/09/2018] [Indexed: 11/18/2022]
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Gioia D, Bertazzo M, Recanatini M, Masetti M, Cavalli A. Dynamic Docking: A Paradigm Shift in Computational Drug Discovery. Molecules 2017; 22:molecules22112029. [PMID: 29165360 PMCID: PMC6150405 DOI: 10.3390/molecules22112029] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/18/2017] [Accepted: 11/19/2017] [Indexed: 12/18/2022] Open
Abstract
Molecular docking is the methodology of choice for studying in silico protein-ligand binding and for prioritizing compounds to discover new lead candidates. Traditional docking simulations suffer from major limitations, mostly related to the static or semi-flexible treatment of ligands and targets. They also neglect solvation and entropic effects, which strongly limits their predictive power. During the last decade, methods based on full atomistic molecular dynamics (MD) have emerged as a valid alternative for simulating macromolecular complexes. In principle, compared to traditional docking, MD allows the full exploration of drug-target recognition and binding from both the mechanistic and energetic points of view (dynamic docking). Binding and unbinding kinetic constants can also be determined. While dynamic docking is still too computationally expensive to be routinely used in fast-paced drug discovery programs, the advent of faster computing architectures and advanced simulation methodologies are changing this scenario. It is feasible that dynamic docking will replace static docking approaches in the near future, leading to a major paradigm shift in in silico drug discovery. Against this background, we review the key achievements that have paved the way for this progress.
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Affiliation(s)
- Dario Gioia
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Universita' di Bologna, via Belmeloro 6, I-40126 Bologna, Italy.
| | - Martina Bertazzo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Universita' di Bologna, via Belmeloro 6, I-40126 Bologna, Italy.
- Computational Sciences, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
| | - Maurizio Recanatini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Universita' di Bologna, via Belmeloro 6, I-40126 Bologna, Italy.
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Universita' di Bologna, via Belmeloro 6, I-40126 Bologna, Italy.
| | - Andrea Cavalli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Universita' di Bologna, via Belmeloro 6, I-40126 Bologna, Italy.
- Computational Sciences, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
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Kaminskyy D, Kryshchyshyn A, Lesyk R. Recent developments with rhodanine as a scaffold for drug discovery. Expert Opin Drug Discov 2017; 12:1233-1252. [PMID: 29019278 DOI: 10.1080/17460441.2017.1388370] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Rhodanines, as one of the 4-thiazolidinones subtypes, are recognized as privileged heterocycles in medicinal chemistry. The main achievements include the development of drug-like molecules with numerous biological activities as well as approved drugs. Among rhodanines, 5-ene-rhodanines are of special interest, and are often claimed as pan assay interference compounds due to Michael acceptor functionality. Areas covered: Herein, the synthetic protocols for rhodanines and their transformation are reviewed. Biological activity is briefly discussed as well as biotargets, mode of actions and optimization directions. Furthermore, the utilization of 5-ene-rhodanines in Michael additions are discussed while both pro and contra arguments have been outlined within medicinal chemistry application. Expert opinion: Rhodanines remain privileged heterocycles in drug discovery. They are accessible building blocks for optimization and transformation into related heterocycles, simplified analogues and fused heterocycles with a thiazolidine framework. Michael acceptor functionality, as well as the thesis about low selectivity towards biotargets of rhodanines, must be confirmed experimentally and it cannot be based on just the presence of conjugated α,β-unsaturated carbonyl. Moreover, the positive aspects of Michael acceptors must be considered as well as their multitarget properties. New criteria for target affinity must be found. In conclusion, rhodanines are generally not problematic per se.
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Affiliation(s)
- Danylo Kaminskyy
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
| | - Anna Kryshchyshyn
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
| | - Roman Lesyk
- a Department of Pharmaceutical, Organic and Bioorganic Chemistry , Danylo Halytsky Lviv National Medical University , Lviv-10 , Ukraine
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Ahmad S, Raza S, Uddin R, Azam SS. Binding mode analysis, dynamic simulation and binding free energy calculations of the MurF ligase from Acinetobacter baumannii. J Mol Graph Model 2017; 77:72-85. [DOI: 10.1016/j.jmgm.2017.07.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 01/16/2023]
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Azam MA, Jupudi S. Insight into the structural requirements of thiophene-3-carbonitriles-based MurF inhibitors by 3D-QSAR, molecular docking and molecular dynamics study. J Recept Signal Transduct Res 2017; 37:522-534. [PMID: 28768454 DOI: 10.1080/10799893.2017.1360354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The discovery of clinically relevant inhibitors against MurF enzyme has proven to be a challenging task. In order to get further insight into the structural features required for the MurF inhibitory activity, we performed pharmacophore and atom-based three-dimensional quantitative structure-activity relationship studies for novel thiophene-3-carbonitriles based MurF inhibitors. The five-feature pharmacophore model was generated using 48 inhibitors having IC50 values ranging from 0.18 to 663 μm. The best-fitted model showed a higher coefficient of determination (R2 = 0.978), cross-validation coefficient (Q2 = 0.8835) and Pearson coefficient (0.9406) at four component partial least-squares factor. The model was validated with external data set and enrichment study. The effectiveness of the docking protocol was validated by docking the co-crystallized ligand into the catalytic pocket of MurF enzyme. Further, binding free energy calculated by the molecular mechanics generalized Born surface area approach showed that van der Waals and non-polar solvation energy terms are the main contributors to ligand binding in the active site of MurF enzyme. A 10-ns molecular dynamic simulation was performed to confirm the stability of the 3ZM6-ligand complex. Four new molecules are also designed as potent MurF inhibitors. These results provide insights regarding the development of novel MurF inhibitors with better binding affinity.
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Affiliation(s)
- Mohammed Afzal Azam
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy (A Constituent College of Jagadguru Sri Sivarathreeswara University, Mysuru) , Udhagamandalam , India
| | - Srikanth Jupudi
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy (A Constituent College of Jagadguru Sri Sivarathreeswara University, Mysuru) , Udhagamandalam , India
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15
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Extra precision docking, free energy calculation and molecular dynamics studies on glutamic acid derivatives as MurD inhibitors. Comput Biol Chem 2017; 69:55-63. [DOI: 10.1016/j.compbiolchem.2017.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 04/18/2017] [Accepted: 05/20/2017] [Indexed: 01/28/2023]
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Swarupa V, Chaudhury A, Krishna Sarma PVG. Effect of 4-methoxy 1-methyl 2-oxopyridine 3-carbamide on Staphylococcus aureus by inhibiting UDP-MurNAc-pentapeptide, peptidyl deformylase and uridine monophosphate kinase. J Appl Microbiol 2017; 122:663-675. [PMID: 27987382 DOI: 10.1111/jam.13378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 02/01/2023]
Abstract
AIMS The present study aimed to investigate the anti-Staphylococcus aureus and anti-biofilm properties of 4-methoxy-1-methyl-2-oxopyridine-3-carbamide (MMOXC) on S. aureus UDP-MurNAc-pentapeptide (MurF), peptidyl deformylase (PDF) and uridine monophosphate kinase (UMPK). METHODS AND RESULTS The in vitro efficacy of MMOXC was evaluated using quantitative polymerase chain reaction, in vitro assays and broth microdilution methods. Further, the minimum inhibitory concentration (MIC), IC50 and zone of inhibition were recorded in addition to the anti-biofilm property. MMOXC inhibited pure recombinant UMPK and PDF enzymes with a Ki of 0·37 and 0·49 μmol l-1 . However Ki was altered for MurF with varying substrates. The MurF Ki for UMT, d-Ala-d-Ala and ATP as substrates was 0·3, 0·25 and 1·4 μmol l-1 , respectively. Real-time PCR analysis showed a significant reduction in PDF and MurF expression which correlated with the MIC90 at 100 μmol l-1 and IC50 in the range 42 ± 1·5 to 50 ± 1 μmol l-1 against all strains tested. At 5 μmol l-1 MMOXC was able completely to remove preformed biofilms of S. aureus and other drug resistant strains. CONCLUSIONS MMOXC was able to kill S. aureus and drug resistant strains tested by inhibiting MurF, UMPK and PDF enzymes and completely obliterated preformed biofilms. SIGNIFICANCE AND IMPACT OF THE STUDY Growth reduction and biofilm removal are prerequisites for controlling S. aureus infections. In this study MMOXC exhibited prominent anti-S. aureus and anti-biofilm properties by blocking cell wall formation, RNA biosynthesis and protein maturation.
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Affiliation(s)
- V Swarupa
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, India
| | - A Chaudhury
- Department of Microbiology, Sri Venkateswara Institute of Medical Sciences, Tirupati, India
| | - P V G Krishna Sarma
- Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, India
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Kumar M, Kaur T, Sharma A. Role of computational efficiency indices and pose clustering in effective decision making: An example of annulated furanones in Pf-DHFR space. Comput Biol Chem 2017; 67:48-61. [PMID: 28049061 DOI: 10.1016/j.compbiolchem.2016.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 11/04/2016] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
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18
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Ganesan A, Coote ML, Barakat K. Molecular dynamics-driven drug discovery: leaping forward with confidence. Drug Discov Today 2017; 22:249-269. [DOI: 10.1016/j.drudis.2016.11.001] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/22/2016] [Accepted: 11/01/2016] [Indexed: 12/11/2022]
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Development of a one-pot assay for screening and identification of Mur pathway inhibitors in Mycobacterium tuberculosis. Sci Rep 2016; 6:35134. [PMID: 27734910 PMCID: PMC5062083 DOI: 10.1038/srep35134] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 09/23/2016] [Indexed: 01/21/2023] Open
Abstract
The cell wall of Mycobacterium tuberculosis (Mtb) consists of peptidoglycan, arabinogalactan and mycolic acids. The cytoplasmic steps in the peptidoglycan biosynthetic pathway, catalyzed by the Mur (A-F) enzymes, involve the synthesis of UDP-n-acetylmuramyl pentapeptide, a key precursor molecule required for the formation of the peptidoglycan monomeric building blocks. Mur enzymes are indispensable for cell integrity and their lack of counterparts in eukaryotes suggests them to be promising Mtb drug targets. However, the caveat is that most of the current assays utilize a single Mur enzyme, thereby identifying inhibitors against only one of the enzymes. Here, we report development of a one-pot assay that reconstructs the entire Mtb Mur pathway in vitro and has the advantage of eliminating the requirement for nucleotide intermediates in the pathway as substrates. The MurA-MurF enzymes were purified and a one-pot assay was developed through optimization of successive coupled enzyme assays using UDP-n-acetylglucosamine as the initial sugar substrate. The assay is biochemically characterized and optimized for high-throughput screening of molecules that could disrupt multiple targets within the pathway. Furthermore, we have validated the assay by performing it to identify D-Cycloserine and furan-based benzene-derived compounds with known Mur ligase inhibition as inhibitors of Mtb MurE and MurF.
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