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de Oliveira MVD, da Costa KS, Silva JRA, Lameira J, Lima AH. Role of UDP-N-acetylmuramic acid in the regulation of MurA activity revealed by molecular dynamics simulations. Protein Sci 2024; 33:e4969. [PMID: 38532715 DOI: 10.1002/pro.4969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024]
Abstract
The peptidoglycan biosynthesis pathway plays a vital role in bacterial cells, and facilitates peptidoglycan layer formation, a fundamental structural component of the bacterial cell wall. The enzymes in this pathway are candidates for antibiotic development, as most do not have mammalian homologues. The UDP-N-acetylglucosamine (UNAG) enolpyruvyl transferase enzyme (MurA) in the peptidoglycan pathway cytoplasmic step is responsible for the phosphoenolpyruvate (PEP)-UNAG catalytic reaction, forming UNAG enolpyruvate and inorganic phosphate. Reportedly, UDP-N-acetylmuramic acid (UNAM) binds tightly to MurA forming a dormant UNAM-PEP-MurA complex and acting as a MurA feedback inhibitor. MurA inhibitors are complex, owing to competitive binding interactions with PEP, UNAM, and UNAG at the MurA active site. We used computational methods to explore UNAM and UNAG binding. UNAM showed stronger hydrogen-bond interactions with the Arg120 and Arg91 residues, which help to stabilize the closed conformation of MurA, than UNAG. Binding free energy calculations using end-point computational methods showed that UNAM has a higher binding affinity than UNAG, when PEP is attached to Cys115. The unbinding process, simulated using τ-random acceleration molecular dynamics, showed that UNAM has a longer relative residence time than UNAG, which is related to several complex dissociation pathways, each with multiple intermediate metastable states. This prevents the loop from opening and exposing the Arg120 residue to accommodate UNAG and potential new ligands. Moreover, we demonstrate the importance of Cys115-linked PEP in closed-state loop stabilization. We provide a basis for evaluating novel UNAM analogues as potential MurA inhibitors. PUBLIC SIGNIFICANCE: MurA is a critical enzyme involved in bacterial cell wall biosynthesis and is involved in antibiotic resistance development. UNAM can remain in the target protein's active site for an extended time compared to its natural substrate, UNAG. The prolonged interaction of this highly stable complex known as the 'dormant complex' comprises UNAM-PEP-MurA and offers insights into antibiotic development, providing potential options against drug-resistant bacteria and advancing our understanding of microbial biology.
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Affiliation(s)
- Maycon Vinicius Damasceno de Oliveira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Kauê S da Costa
- Institute of Biodiversity, Federal University of Western Pará, Santarém, Pará, Brazil
| | - José Rogério A Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Anderson H Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, Brazil
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2
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Verma A, Kumar V, Naik B, Masood Khan J, Singh P, Erik Joakim Saris P, Gupta S. Screening and molecular dynamics simulation of compounds inhibiting MurB enzyme of drug-resistant Mycobacterium tuberculosis: An in-silico approach. Saudi J Biol Sci 2023; 30:103730. [PMID: 37483837 PMCID: PMC10362793 DOI: 10.1016/j.sjbs.2023.103730] [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: 05/27/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 07/25/2023] Open
Abstract
Mycobacterium tuberculosis (MTB) is becoming more and more resistant to drugs and it is a common problem, making current antimicrobials ineffective and highlighting the need for new TB drugs. One of the promising targets for treating MTB is MurB enzymes. This study aimed to identify potential inhibitors of MurB enzymes in M. tuberculosis, as drug resistance among MTB is a significant problem. Attempts are being made to conduct a virtual screening of 30,417 compounds, and thirty-two compounds were chosen for further analysis based on their binding conformations. The selected compounds were assessed for their drug-likeness, pharmacokinetics, and physiochemical characteristics, and seven compounds with binding energy lower than flavin (FAD) were identified. Further, molecular dynamics simulation analysis of these seven compounds found that four of them, namely DB12983, DB15688, ZINC084726167, and ZINC254071113 formed stable complexes with the MurB binding site, exhibiting promising inhibitory activity. These compounds have not been mentioned in any other study, indicating their novelty. The study suggests that these four compounds could be promising candidates for treating MTB, but their effectiveness needs to be validated through in vitro and in vivo experiments. Overall, the findings of this study provide new insight into potential drug targets and candidates for combating drug-resistant MTB.
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Affiliation(s)
- Ankit Verma
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, India 248140
| | - Vijay Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, India 248140
| | - Bindu Naik
- Department of Food Science and Technology, Graphic Era (Deemed to be University), Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
| | - Pallavi Singh
- Department of Biotechnology, Graphic Era (Deemed to be University), Bell Road, Clement town, 248002 Dehradun, Uttarakhand, India
| | - Per Erik Joakim Saris
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Finland
| | - Sanjay Gupta
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, India 248140
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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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Minjárez-Sáenz M, Martínez-Júlvez M, Yruela I, Medina M. Mining the Flavoproteome of Brucella ovis, the Brucellosis Causing Agent in Ovis aries. Microbiol Spectr 2022; 10:e0229421. [PMID: 35315701 PMCID: PMC9045290 DOI: 10.1128/spectrum.02294-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/19/2022] [Indexed: 11/20/2022] Open
Abstract
Flavoproteins are a diverse class of proteins that are mostly enzymes and contain as cofactors flavin mononucleotide (FMN) and/or flavin adenine dinucleotide (FAD), which enable them to participate in a wide range of physiological reactions. We have compiled 78 potential proteins building the flavoproteome of Brucella ovis (B. ovis), the causative agent of ovine brucellosis. The curated list of flavoproteins here reported is based on (i) the analysis of sequence, structure and function of homologous proteins, and their classification according to their structural domains, clans, and expected enzymatic functions; (ii) the constructed phylogenetic trees of enzyme functional classes using 19 Brucella strains and 26 pathogenic and/or biotechnological relevant alphaproteobacteria together with B. ovis; and (iii) the evaluation of the genetic context for each entry. Candidates account for ∼2.7% of the B. ovis proteome, and 75% of them use FAD as cofactor. Only 55% of these flavoproteins belong to the core proteome of Brucella and contribute to B. ovis processes involved in maintenance activities, survival and response to stress, virulence, and/or infectivity. Several of the predicted flavoproteins are highly divergent in Brucella genus from revised proteins and for them it is difficult to envisage a clear function. This might indicate modified catalytic activities or even divergent processes and mechanisms still not identified. We have also detected the lack of some functional flavoenzymes in B. ovis, which might contribute to it being nonzoonotic. Finally, potentiality of B. ovis flavoproteome as the source of antimicrobial targets or biocatalyst is discussed. IMPORTANCE Some microorganisms depend heavily on flavin-dependent activities, but others maintain them at a minimum. Knowledge about flavoprotein content and functions in different microorganisms will help to identify their metabolic requirements, as well as to benefit either industry or health. Currently, most flavoproteins from the sheep pathogen Brucella ovis are only automatically annotated in databases, and only two have been experimentally studied. Indeed, certain homologues with unknown function are not characterized, and they might relate to still not identified mechanisms or processes. Our research has identified 78 members that comprise its flavoproteome, 76 of them flavoenzymes, which mainly relate to bacteria survival, virulence, and/or infectivity. The list of flavoproteins here presented allows us to better understand the peculiarities of Brucella ovis and can be applied as a tool to search for candidates as new biocatalyst or antimicrobial targets.
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Affiliation(s)
- Martha Minjárez-Sáenz
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology “GBsC” (BIFI, Unizar) Joint Unit to CSIC, Zaragoza, Spain
| | - Inmaculada Yruela
- Estación Experimental de Aula Dei, CSIC, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology “GBsC” (BIFI, Unizar) Joint Unit to CSIC, Zaragoza, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology “GBsC” (BIFI, Unizar) Joint Unit to CSIC, Zaragoza, Spain
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Yang L, Hu X, Chai X, Ye Q, Pang J, Li D, Hou T. Opportunities for overcoming tuberculosis: Emerging targets and their inhibitors. Drug Discov Today 2021; 27:326-336. [PMID: 34537334 DOI: 10.1016/j.drudis.2021.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/24/2021] [Accepted: 09/10/2021] [Indexed: 12/28/2022]
Abstract
Tuberculosis (TB), an airborne infectious disease mainly caused by Mycobacterium tuberculosis (Mtb), remains a leading cause of human morbidity and mortality worldwide. Given the alarming rise of resistance to anti-TB drugs and latent TB infection (LTBI), new targets and novel bioactive compounds are urgently needed for the treatment of this disease. We provide an overview of the recent advances in anti-TB drug discovery, emphasizing several newly validated targets for which an inhibitor has been reported in the past five years. Our review presents several attractive directions that have potential for the development of next-generation therapies.
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Affiliation(s)
- Liu Yang
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xueping Hu
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xin Chai
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qing Ye
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jinping Pang
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dan Li
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Lab of Computer-aided Design and Computer Graphics (CAD&CG), Zhejiang University, Hangzhou, Zhejiang 310058, China.
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6
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Shinde Y, Ahmad I, Surana S, Patel H. The Mur Enzymes Chink in the Armour of Mycobacterium tuberculosis cell wall. Eur J Med Chem 2021; 222:113568. [PMID: 34118719 DOI: 10.1016/j.ejmech.2021.113568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 02/02/2023]
Abstract
TUBERCULOSIS: (TB) transmitted by Mycobacterium tuberculosis (Mtb) is one of the top 10 causes of death globally. Currently, the widespread occurrence of resistance toward Mtb strains is becoming a significant concern to public health. This scenario exaggerated the need for the discovery of novel targets and their inhibitors. Targeting the "Mtb cell wall peptidoglycan synthesis" is an attractive strategy to overcome drug resistance. Mur enzymes (MurA-MurF) play essential roles in the peptidoglycan synthesis by catalyzing the ligation of key amino acid residues to the stem peptide. These enzymes are unique and confined to the eubacteria and are absent in humans, representing potential targets for anti-tubercular drug discovery. Mtb Mur ligases with the same catalytic mechanism share conserved amino acid regions and structural features that can conceivably exploit for the designing of the inhibitors, which can simultaneously target more than one isoforms (MurC-MurF) of the enzyme. In light of these findings in the current review, we have discussed the recent advances in medicinal chemistry of Mtb Mur enzymes (MurA-MurF) and their inhibitors, offering attractive multi-targeted strategies to combat the problem of drug-resistant in M. tuberculosis.
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Affiliation(s)
- Yashodeep Shinde
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Sanjay Surana
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Harun Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India.
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7
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Kumari M, Subbarao N. Identification of novel multitarget antitubercular inhibitors against mycobacterial peptidoglycan biosynthetic Mur enzymes by structure-based virtual screening. J Biomol Struct Dyn 2021; 40:8185-8196. [PMID: 33826470 DOI: 10.1080/07391102.2021.1908913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Current therapeutic strategies for several diseases, including Mycobacterium tuberculosis infection, have evolved from an initial single-target treatment to a multitarget one. A multitarget antitubercular drugs targeting different mycobacterial proteins are more effective at suppressing bacterial growth. In this study, a high throughput virtual screening was performed to identify hits to the potential antitubercular multitarget: murA, murB, murC, murD, murE, murF, murG and murI from M. tuberculosis that is involved in peptidoglycan biosynthesis. In the virtual screening, we were docked 56,400 compounds of the ChEMBL antimycobacterial library and re-scored and identified the top 10 ranked compounds as antitubercular drug candidates. Further, the best common docked complex CHEMBL446262 was subjected to molecular dynamics simulation to understand the molecule's stability in the presence of an active site environment. After that, we have calculated binding free energy the top-ranked docked complexes using the MM/PBSA method. These ligands exhibited the highest binding affinity; find out novel drug-likeness might show the M. tuberculosis effect's inhibitor by interacting with multitarget Mur enzymes. New antitubercular therapies that include multitarget drugs may have higher efficacy than single-target medicines and provide a more straightforward antitubercular therapy regimen.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madhulata Kumari
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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8
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Structure-based inhibitor screening of natural products against NSP15 of SARS-CoV-2 revealed thymopentin and oleuropein as potent inhibitors. ACTA ACUST UNITED AC 2021; 12:71-80. [PMID: 33776343 PMCID: PMC7985738 DOI: 10.1007/s42485-021-00059-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 12/26/2022]
Abstract
Coronaviruses are enveloped, non-segmented positive-sense RNA viruses with the largest genome among RNA viruses. Their genome contains a large replicase ORF which encodes nonstructural proteins (NSPs), structural, and accessory genes. NSP15 is a nidoviral RNA uridylate-specific endoribonuclease (NendoU) with C-terminal catalytic domain. The endoribonuclease activity of NSP15 interferes with the innate immune response of the host. Here, we screened Selleckchem Natural product database of the compounds against NSP15, and we found that thymopentin and oleuropein displayed highest binding energies. The binding of these molecules was further validated by molecular dynamic simulations that revealed them as very stable complexes. These drugs might serve as effective counter molecules in the reduction of virulence of this virus; may be more effective if treated in combination with replicase inhibitors. Future validation of both these inhibitors is worth the consideration for patients being treated for COVID-19.
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9
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Kumari P, Vijayan R, Gourinath S. Structural analysis of EhPSP in complex with 3-phosphoglyceric acid from Entamoeba histolytica reveals a basis for its lack of phosphoglycerate mutase activity. Int J Biol Macromol 2021; 178:1-10. [PMID: 33631257 DOI: 10.1016/j.ijbiomac.2021.02.153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/21/2021] [Accepted: 02/20/2021] [Indexed: 01/11/2023]
Abstract
Entamoeba histolytica phosphoserine phosphatase (EhPSP), a regulatory enzyme in the serine biosynthetic pathway, is also a structural homolog of cofactor-dependent phosphoglycerate mutase (dPGM). However, despite sharing many of its catalytic residues with dPGM, EhPSP displays no significant mutase activity. In the current work, we determined a crystal structure of EhPSP in complex with 3-PGA to 2.5 Å resolution and observed striking differences between the orientation of 3-PGA bound to EhPSP and that to its other homologous structures. We also performed computational modeling and simulations of the intermediate 2,3-bisphosphoglyceric acid into the active site of EhPSP to better understand its mechanistic details. Based on these results and those of a similar study with the dPGMs from E. coli and B. pseudomallei, the affinity of EhPSP for 2,3-BPG was concluded to be lower than those of the other proteins. Moreover, a different set of 2,3-BPG interacting residues was observed in EhPSP compared to dPGMs, with all of the crucial interacting residues of dPGMs either missing or substituted with weakly interacting residues. This study has expanded our understanding, at the structural level, of the inability of EhPSP to catalyze the mutase reaction and has strengthened earlier conclusions indicating it to be a true phosphatase.
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Affiliation(s)
- Poonam Kumari
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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10
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Kumar S, Vijayan R, Dash AK, Gourinath S, Tyagi RK. Nuclear receptor SHP dampens transcription function and abrogates mitotic chromatin association of PXR and ERα via intermolecular interactions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194683. [PMID: 33444783 DOI: 10.1016/j.bbagrm.2020.194683] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 11/29/2020] [Accepted: 12/29/2020] [Indexed: 01/07/2023]
Abstract
Mitosis is a cellular process that produces two identical progenies. Genome-wide transcription is believed to be silenced during mitosis. However, some transcription factors have been reported to associate with the mitotic chromatin to uphold a role in 'gene-bookmarking'. Here, we investigated the dynamic role of nuclear receptor SHP during cell cycle, and observed intermolecular interactions with PXR and ERα. This was reflected in altered subcellular localization, transcription function and mitotic chromatin behavior of these receptors. Subsequently, by in silico and live cell imaging approaches we identified the minimal domain(s) and crucial amino-acid residues required for such receptor-receptor interactions. It was apparent that both PXR/ERα interact with SHP to translocate cytoplasmic RFP-tagged SHP into the nucleus. In addition, during mitosis SHP interacted with some of the key nuclear receptors, altering partners, as well as, its own relationship with mitotic chromatin. SHP displaced a major fraction of PXR and ERα from the mitotic chromatin while promoted its own weak association reflected in its binding. Since SHP lacks DBD this association is attributed to receptor-receptor interactions rather than SHP-DNA interactions. The abrogation of PXR and ERα from the mitotic chromatin by SHP implies potential implications in regulation of gene bookmarking events in cellular development. Overall, it is concluded that intermolecular interactions between SHP and partner PXR/ERα result in attenuation of target promoter activities. It is proposed that SHP may act as an indirect physiological regulator and functions in a hog-tie manner by displacing the interacting transcription factor from gene regulatory sites.
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Affiliation(s)
- Sudhir Kumar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | | | - Amit K Dash
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Samudrala Gourinath
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rakesh K Tyagi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India.
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11
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Deciphering the interaction of benzoxaborole inhibitor AN2690 with connective polypeptide 1 (CP1) editing domain of Leishmania donovani leucyl-tRNA synthetase. J Biosci 2020. [DOI: 10.1007/s12038-020-00031-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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12
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Batt SM, Burke CE, Moorey AR, Besra GS. Antibiotics and resistance: the two-sided coin of the mycobacterial cell wall. Cell Surf 2020; 6:100044. [PMID: 32995684 PMCID: PMC7502851 DOI: 10.1016/j.tcsw.2020.100044] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 01/07/2023] Open
Abstract
Mycobacterium tuberculosis, the bacterium responsible for tuberculosis, is the global leading cause of mortality from an infectious agent. Part of this success relies on the unique cell wall, which consists of a thick waxy coat with tightly packed layers of complexed sugars, lipids and peptides. This coat provides a protective hydrophobic barrier to antibiotics and the host's defences, while enabling the bacterium to spread efficiently through sputum to infect and survive within the macrophages of new hosts. However, part of this success comes at a cost, with many of the current first- and second-line drugs targeting the enzymes involved in cell wall biosynthesis. The flip side of this coin is that resistance to these drugs develops either in the target enzymes or the activation pathways of the drugs, paving the way for new resistant clinical strains. This review provides a synopsis of the structure and synthesis of the cell wall and the major current drugs and targets, along with any mechanisms of resistance.
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Affiliation(s)
- Sarah M. Batt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Christopher E. Burke
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alice R. Moorey
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Gurdyal S. Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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13
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Maitra A, Munshi T, Healy J, Martin LT, Vollmer W, Keep NH, Bhakta S. Cell wall peptidoglycan in Mycobacterium tuberculosis: An Achilles' heel for the TB-causing pathogen. FEMS Microbiol Rev 2020; 43:548-575. [PMID: 31183501 PMCID: PMC6736417 DOI: 10.1093/femsre/fuz016] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/07/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB), caused by the intracellular pathogen Mycobacterium tuberculosis, remains one of the leading causes of mortality across the world. There is an urgent requirement to build a robust arsenal of effective antimicrobials, targeting novel molecular mechanisms to overcome the challenges posed by the increase of antibiotic resistance in TB. Mycobacterium tuberculosis has a unique cell envelope structure and composition, containing a peptidoglycan layer that is essential for maintaining cellular integrity and for virulence. The enzymes involved in the biosynthesis, degradation, remodelling and recycling of peptidoglycan have resurfaced as attractive targets for anti-infective drug discovery. Here, we review the importance of peptidoglycan, including the structure, function and regulation of key enzymes involved in its metabolism. We also discuss known inhibitors of ATP-dependent Mur ligases, and discuss the potential for the development of pan-enzyme inhibitors targeting multiple Mur ligases.
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Affiliation(s)
- Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Tulika Munshi
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Jess Healy
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Liam T Martin
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Nicholas H Keep
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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14
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Crystal structure of O-Acetylserine sulfhydralase (OASS) isoform 3 from Entamoeba histolytica: Pharmacophore-based virtual screening and validation of novel inhibitors. Eur J Med Chem 2020; 192:112157. [PMID: 32145643 DOI: 10.1016/j.ejmech.2020.112157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/03/2020] [Accepted: 02/17/2020] [Indexed: 01/09/2023]
Abstract
The l-cysteine is crucial for growth, survival, defense against oxidative stress, and pathogenesis of Entamoeba histolytica. The de novo biosynthesis of l-cysteine in E. histolytica, has a two-step pathway, where O-acetylserine sulfhydrylase (OASS) catalyses the last step by converting OAS to l-cysteine. This pathway is absent in humans and hence represents a promising target for novel therapeutics. E. histolytica expresses three isoforms of OASS and knockdown studies showed the importance of these enzymes for the survival of the pathogen. Here, we report the crystal structure of OASS isoform 3 from E. histolytica to 1.54 Å resolution. The active site geometries and kinetics of EhOASS3 and EhOASS1 structures were found to be very similar. Small-molecule libraries were screened against EhOASS3 and compounds were shortlisted based on the docking scores. F3226-1387 showed best inhibition with IC50 of 38 μM against EhOASS3 and was able to inhibit the growth of the organism to 72%.
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15
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Nirwan S, Chahal V, Kakkar R. Structure-based virtual screening, free energy of binding and molecular dynamics simulations to propose novel inhibitors of Mtb-MurB oxidoreductase enzyme. J Biomol Struct Dyn 2020; 39:656-671. [DOI: 10.1080/07391102.2020.1712258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sonam Nirwan
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Varun Chahal
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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16
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Jukič M, Hrast M, Patin D, Ogorevc E, Barreteau H, Gobec S. Virtual screening approach and biochemical evaluation on MurB. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cdc.2019.100276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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17
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Biochemical and biophysical characterization of the smallest pyruvate kinase from Entamoeba histolytica. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140296. [PMID: 31676451 DOI: 10.1016/j.bbapap.2019.140296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 01/07/2023]
Abstract
Entamoeba histolytica infection is highly prevalent in developing countries across the globe. The ATP synthesis in this pathogen is solely dependent on the glycolysis pathway where pyruvate kinase (Pyk) catalyzes the final reaction. Here, we have cloned, overexpressed and purified the pyruvate kinase (EhPyk) from E. histolytica. EhPyk is the shortest currently known Pyk till date as it contains only two of the three characterized domains when compared to the other homologues and our phylogenetic analysis places it on a distinct branch from the known type I/II Pyks. Our purification results suggested that it exists as a homodimer in solution. The kinetic characterization showed that EhPyk has maximum activity at pH 7.5 where it exhibited Michaelis-Menten's kinetics for phosphoenolpyruvate with a Km of 0.23 mM, and it lost its activity at both the acidic pH 4.0 and basic pH 10.0. We also determined the key secondary structural elements of EhPyk at different pH values. MD simulation of EhPyk structure at different pH values suggested that it is most stable at pH 7.0, while least stable at pH 10.0 followed by pH 4.0. Together, our computational simulations correlate well with the experimental studies. In summary, this study expands the current understanding of the EhPyk identified earlier in the amoebic genome and provides the first characterization of this bacterially expressed protein.
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18
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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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19
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Rani J, Silla Y, Borah K, Ramachandran S, Bajpai U. Repurposing of FDA-approved drugs to target MurB and MurE enzymes in Mycobacterium tuberculosis. J Biomol Struct Dyn 2019; 38:2521-2532. [PMID: 31244382 DOI: 10.1080/07391102.2019.1637280] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) is one amongst the top 10 causes of death worldwide. The growing rise in antibiotic resistance compounded with slow and expensive drug discovery has further aggravated the situation. 'Drug repurposing' is a promising approach where known drugs are examined for a new indication. In the present study, we have attempted to identify drugs that could target MurB and MurE enzymes involved in the muramic acid synthesis pathway (Mur Pathway) in Mtb. FDA-approved drugs from two repositories i.e. Drug Bank (1932 drugs) and e-LEA3D (1852 drugs) were screened against these proteins. Several criteria were applied to study the protein-drug interactions and the consensus drugs were further studied by molecular dynamics (MD) simulation. Our study found Sulfadoxine (-7.3 kcal/mol) and Pyrimethamine (-7.8 kcal/mol) to show stable interaction with MurB while Lifitegrast (-10.5 kcal/mol) and Sildenafil (-9.1 kcal/mol) showed most reliable interaction with MurE. Furthermore, binding free energy (ΔGbind), RMSD and RMSF data and the number of hydrogen bonds corroborated the stability of interactions and hence these drugs for repurposing should be explored further.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jyoti Rani
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India.,G. N. Ramachandran Knowledge of Centre, Council of Scientific and Industrial Research - Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Yumnam Silla
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, India
| | - Kasmika Borah
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, India
| | - Srinivasan Ramachandran
- G. N. Ramachandran Knowledge of Centre, Council of Scientific and Industrial Research - Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India
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20
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Gao T, Yuan F, Liu Z, Liu W, Zhou D, Yang K, Duan Z, Guo R, Liang W, Hu Q, Tian Y, Zhou R. MnmE, a Central tRNA-Modifying GTPase, Is Essential for the Growth, Pathogenicity, and Arginine Metabolism of Streptococcus suis Serotype 2. Front Cell Infect Microbiol 2019; 9:173. [PMID: 31179247 PMCID: PMC6543552 DOI: 10.3389/fcimb.2019.00173] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/08/2019] [Indexed: 12/11/2022] Open
Abstract
Streptococcus suis is an important pathogen in pigs and can also cause severe infections in humans. However, little is known about proteins associated with cell growth and pathogenicity of S. suis. In this study, a guanosine triphosphatase (GTPase) MnmE homolog was identified in a Chinese isolate (SC19) that drives a tRNA modification reaction. A mnmE deletion strain (ΔmnmE) and a complementation strain (CΔmnmE) were constructed to systematically decode the characteristics and functions of MnmE both in vitro and in vivo studies via proteomic analysis. Phenotypic analysis revealed that the ΔmnmE strain displayed deficient growth, attenuated pathogenicity, and perturbation of the arginine metabolic pathway mediated by the arginine deiminase system (ADS). Consistently, tandem mass tag -based quantitative proteomics analysis confirmed that 365 proteins were differentially expressed (174 up- and 191 down-regulated) between strains ΔmnmE and SC19. Many proteins associated with DNA replication, cell division, and virulence were down-regulated. Particularly, the core enzymes of the ADS were significantly down-regulated in strain ΔmnmE. These data also provide putative molecular mechanisms for MnmE in cell growth and survival in an acidic environment. Therefore, we propose that MnmE, by its function as a central tRNA-modifying GTPase, is essential for cell growth, pathogenicity, as well as arginine metabolism of S. suis.
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Affiliation(s)
- Ting Gao
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Fangyan Yuan
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Zewen Liu
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wei Liu
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Danna Zhou
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Keli Yang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Zhengying Duan
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Rui Guo
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wan Liang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Qiao Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Cooperative Innovation Center of Sustainable Pig Production, Wuhan, China
| | - Yongxiang Tian
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture and Rural Affairs), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Cooperative Innovation Center of Sustainable Pig Production, Wuhan, China
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21
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Waziri F, Vijayan R, Sahar T, Anwar S, Gourinath S, Jain SK, Wajid S. In silico elucidation of novel anticancer lead molecules targeting human prostate specific gene-1 protein. J Biomol Struct Dyn 2018; 37:2118-2124. [DOI: 10.1080/07391102.2018.1477623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Farheen Waziri
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | | | - Tahreem Sahar
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Shadab Anwar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Swatantra Kumar Jain
- Department of Biochemistry, Hamdard Institute of Medical Sciences and Research, Jamia Hamdard, New Delhi, India
| | - Saima Wajid
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
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22
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Jukič M, Gobec S, Sova M. Reaching toward underexplored targets in antibacterial drug design. Drug Dev Res 2018; 80:6-10. [PMID: 30312991 DOI: 10.1002/ddr.21465] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/13/2018] [Accepted: 08/15/2018] [Indexed: 01/03/2023]
Abstract
The increase of antimicrobial resistance necessitates the renewal and strong research involvement in antibacterial drug design. In the following work, we comment on the key approaches used in development of new antibacterials, focusing on intracellular therapeutic targets that have been so far mostly underexplored: the enzymes of the Mur pathway MurA to MurF. We identify common obstacles observed during research on MurA, MurB, and Mur ligases inhibitors and their development into potential antibacterial compounds, and discern several approaches and solutions to tackle the whole-cell activity of designed compounds. Furthermore, we consolidate recent literature reports and encourage the further research on Mur enzymes.
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Affiliation(s)
- Marko Jukič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Matej Sova
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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23
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Gupta RS. Impact of Genomics on Clarifying the Evolutionary Relationships amongst Mycobacteria: Identification of Molecular Signatures Specific for the Tuberculosis-Complex of Bacteria with Potential Applications for Novel Diagnostics and Therapeutics. High Throughput 2018; 7:ht7040031. [PMID: 30279355 PMCID: PMC6306742 DOI: 10.3390/ht7040031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 12/31/2022] Open
Abstract
An alarming increase in tuberculosis (TB) caused by drug-resistant strains of Mycobacterium tuberculosis has created an urgent need for new antituberculosis drugs acting via novel mechanisms. Phylogenomic and comparative genomic analyses reviewed here reveal that the TB causing bacteria comprise a small group of organisms differing from all other mycobacteria in numerous regards. Comprehensive analyses of protein sequences from mycobacterial genomes have identified 63 conserved signature inserts and deletions (indels) (CSIs) in important proteins that are distinctive characteristics of the TB-complex of bacteria. The identified CSIs provide potential means for development of novel diagnostics as well as therapeutics for the TB-complex of bacteria based on four key observations: (i) The CSIs exhibit a high degree of exclusivity towards the TB-complex of bacteria; (ii) Earlier work on CSIs provide evidence that they play important/essential functions in the organisms for which they exhibit specificity; (iii) CSIs are located in surface-exposed loops of the proteins implicated in mediating novel interactions; (iv) Homologs of the CSIs containing proteins, or the CSIs in such homologs, are generally not found in humans. Based on these characteristics, it is hypothesized that the high-throughput virtual screening for compounds binding specifically to the CSIs (or CSI containing regions) and thereby inhibiting the cellular functions of the CSIs could lead to the discovery of a novel class of drugs specifically targeting the TB-complex of organisms.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada.
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24
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Raghavendra T, Patil S, Mukherjee R. Peptidoglycan in Mycobacteria: chemistry, biology and intervention. Glycoconj J 2018; 35:421-432. [DOI: 10.1007/s10719-018-9842-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/20/2018] [Accepted: 09/05/2018] [Indexed: 01/07/2023]
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