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Li M, Liu X, Li D, Ding J, Yang F, Huo Z, Yan X. The energy metabolism and transcriptomic responses of the Manila clam (Ruditapes philippinarum) under the low-temperature stress. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 51:101259. [PMID: 38797003 DOI: 10.1016/j.cbd.2024.101259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Low temperature in winter poses a threat to the Manila clam Ruditapes philippinarum in North China. However, a number of low-temperature-tolerant clams could survive such condition. It is therefore of interest to explore the survival mechanisms underlying the cold tolerance of R. philippinarum. The Zebra II population of R. philippinarum (Zebra II) from North China and the native Putian population from South China were used as experimental materials. Both populations were stressed with low-temperature and the differences in their survival rates, energy metabolism and transcriptional responses were compared. The results shown that after cold treatment at -1.9 °C, survival rate of Zebra II was higher than that of the Putian group. For both groups, the respiration, ammonia excretion, and ingestion rates continuously decreased till 0 with reductions temperature. In addition, RNA-seq revealed that as compared with the Putian group, there were 3682 up-regulated differentially expressed genes (DEGs) and 3361 down-regulated DEGs in Zebra II group. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DEGs were mostly enriched in the purine, pyrimidine, and pyruvate metabolism pathways in Zebra II under low-temperature stress. Furthermore, qRT-PCR analysis further confirmed that Zebra II responded to low-temperature stress through upregulating genes involved in purine, pyrimidine, and pyruvate metabolism pathways. Taken together, all these results indicated that Zebra II has higher cold tolerance than the Putian group. Therefore, Zebra II is capable for overwintering in the intertidal zone of North China.
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Affiliation(s)
- Mingren Li
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian 116023, China
| | - Xiande Liu
- Fisheries College of Jimei University, Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Xiamen 361021, China
| | - Dongdong Li
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian 116023, China.
| | - Jianfeng Ding
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian 116023, China
| | - Feng Yang
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian 116023, China
| | - Zhongming Huo
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian 116023, China.
| | - Xiwu Yan
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian 116023, China
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2
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Chikhale RV, Pawar SP, Kolpe MS, Shinde OD, Dahlous KA, Mohammad S, Patil PC, Bhowmick S. Identification of mycobacterial Thymidylate kinase inhibitors: a comprehensive pharmacophore, machine learning, molecular docking, and molecular dynamics simulation studies. Mol Divers 2024:10.1007/s11030-024-10967-w. [PMID: 39152354 DOI: 10.1007/s11030-024-10967-w] [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: 04/21/2024] [Accepted: 08/08/2024] [Indexed: 08/19/2024]
Abstract
Thymidylate kinase (TMK) is a pivotal enzyme in Mycobacterium tuberculosis (Mtb), crucial for phosphorylating thymidine monophosphate (dTMP) to thymidine diphosphate (dTDP), thereby playing a critical role in DNA biosynthesis. Dysregulation or inhibition of TMK activity disrupts DNA replication and cell division, making it an attractive target for anti-tuberculosis drug development. In this study, the statistically validated pharmacophore mode was developed from a set of known TMK inhibitors. Further, the robust pharmacophore was considered for screening the Enamine database. The chemical space was reduced through multiple molecular docking approaches, pharmacokinetics, and absolute binding energy estimation. Two different molecular docking algorithms favor the strong binding affinity of the proposed molecules towards TMK. Machine learning-based absolute binding energy also showed the potentiality of the proposed molecules. The binding interactions analysis exposed the strong binding affinity between the proposed molecules and active site amino residues of TMK. Several statistical parameters from all atoms MD simulation explained the stability between proposed molecules and TMK in the dynamic states. The MM-GBSA approach also found a strong binding affinity for each proposed molecule. Therefore, the proposed molecules might be crucial TMK inhibitors for managing Mtb inhibition subjected to in vitro/in vivo validations.
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Affiliation(s)
- Rupesh V Chikhale
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, UK.
| | - Surbhi Pravin Pawar
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth (Deemed to be University), Pune-Satara Road, Pune, India
| | - Mahima Sudhir Kolpe
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
| | - Omkar Dilip Shinde
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth (Deemed to be University), Pune-Satara Road, Pune, India
| | - Kholood A Dahlous
- Department of Chemistry, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Saikh Mohammad
- Department of Chemistry, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Pritee Chunarkar Patil
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth (Deemed to be University), Pune-Satara Road, Pune, India
| | - Shovonlal Bhowmick
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
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3
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Guo Y, Dong X, Li H, Lin W, Cao L, Li D, Zhang Y, Jin J, Tong Y, Liu Z. Efficient Broad-Spectrum Cyanophage Function Module Mining. Microorganisms 2024; 12:1578. [PMID: 39203420 PMCID: PMC11356776 DOI: 10.3390/microorganisms12081578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 09/03/2024] Open
Abstract
Cyanobacterial harmful algal blooms (CyanoHABs) cause health and environmental effects worldwide. Cyanophage is a virus that exclusively infects cyanobacteria. Using cyanophages to control blooms is the latest biological control method. However, little research on the genomics of cyanophages and the presence of numerous proteins with unidentified functions in cyanophage genomes pose challenges for their practical application and comprehensive investigation. We selected the broad-spectrum and efficient cyanophage YongM for our study. On the one hand, through rational analysis, we analyze essential genes, establish the minimal cyanophage genome and single essential gene modules, and examine the impact of essential modules on growth. Additionally, we conducted ultraviolet mutagenesis on YongM to generate more efficient cyanophages' critical modules through random mutagenesis. Then, we sequenced and analyzed the functionality of the mutational gene modules. These findings highlight several gene modules that contribute to a deeper understanding of the functional components within cyanophage genomes.
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Affiliation(s)
- Yujing Guo
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaoxiao Dong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Huiying Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Lin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lei Cao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Dengfeng Li
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo 315211, China;
| | - Yiming Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jin Jin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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4
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Tanvir R, Ijaz S, Sajid I, Hasnain S. Multifunctional in vitro, in silico and DFT analyses on antimicrobial BagremycinA biosynthesized by Micromonospora chokoriensis CR3 from Hieracium canadense. Sci Rep 2024; 14:10976. [PMID: 38745055 PMCID: PMC11093986 DOI: 10.1038/s41598-024-61490-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 05/06/2024] [Indexed: 05/16/2024] Open
Abstract
Among the actinomycetes in the rare genera, Micromonospora is of great interest since it has been shown to produce novel therapeutic compounds. Particular emphasis is now on its isolation from plants since its population from soil has been extensively explored. The strain CR3 was isolated as an endophyte from the roots of Hieracium canadense, and it was identified as Micromonospora chokoriensis through 16S gene sequencing and phylogenetic analysis. The in-vitro analysis of its extract revealed it to be active against the clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) and Candida tropicalis (15 mm). No bioactivity was observed against Gram-negative bacteria, Escherichia coli ATCC 25922, and Klebsiella pneumoniae ATCC 706003. The Micromonospora chokoriensis CR3 extract was also analyzed through the HPLC-DAD-UV-VIS resident database, and it gave a maximum match factor of 997.334 with the specialized metabolite BagremycinA (BagA). The in-silico analysis indicated that BagA strongly interacted with the active site residues of the sterol 14-α demethylase and thymidylate kinase enzymes, with the lowest binding energies of - 9.7 and - 8.3 kcal/mol, respectively. Furthermore, the normal mode analysis indicated that the interaction between these proteins and BagA was stable. The DFT quantum chemical properties depicted BagA to be reasonably reactive with a HOMO-LUMO gap of (ΔE) of 4.390 eV. BagA also passed the drug-likeness test with a synthetic accessibility score of 2.06, whereas Protox-II classified it as a class V toxicity compound with high LD50 of 2644 mg/kg. The current study reports an endophytic actinomycete, M. chokoriensis, associated with H. canadense producing the bioactive metabolite BagA with promising antimicrobial activity, which can be further modified and developed into a safe antimicrobial drug.
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Affiliation(s)
- Rabia Tanvir
- Institute of Microbiology (IOM), University of Veterinary and Animal Sciences (UVAS), Lahore, 54000, Punjab, Pakistan.
| | - Saadia Ijaz
- Department of Microbiology and Molecular Genetics, The Women University, Multan, 66000, Punjab, Pakistan
| | - Imran Sajid
- Institute of Microbiology and Molecular Genetics (IMMG), University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Punjab, Pakistan
| | - Shahida Hasnain
- Institute of Microbiology and Molecular Genetics (IMMG), University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Punjab, Pakistan
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5
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Ali Y, Khan AA, Alanazi AM, Abdikakharovich SA, Shah JA, Ren ZG, Khattak S. Identification of the myxobacterial secondary metabolites Aurachin A and Soraphinol A as promising inhibitors of thymidylate kinase of the Monkeypox virus. Mol Divers 2024:10.1007/s11030-023-10764-x. [PMID: 38183513 DOI: 10.1007/s11030-023-10764-x] [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: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 01/08/2024]
Abstract
Thymidylate kinase (TMPK) of monkeypox virus (MPXV) has emerged as a promising target for potential therapeutics due to its significant role in pyrimidine metabolism. While smallpox drugs are advised for treating monkeypox, the European Medicine Agency has sanctioned Tecovirimat due to its potent nanomolar activity. Nonetheless, there is a need for monkeypox-specific therapeutic options. In this work, we employed docking-based virtual screening and molecular dynamics (MD) simulations to identify myxobacterial secondary metabolites as promising anti-viral natural compounds capable of inhibiting thymidylate kinase. The computational pharmacokinetics and manual curation of top-scoring compounds identified six lead compounds that were compared in terms of protein-ligand contacts and protein-essential dynamics. The study shows that among the six candidates, Aurachin A and the Soraphinol analogues such as Soraphinol A and Soraphinol C remain very stable compared to other compounds, enabling the active site integrity via a stable dynamics pattern. We also show that other compounds such as Phenoxan, Phenylnannolone C, and 8E-Aurafuron B remain unstable and have a negative impact on the active site integrity and may not be suitable binders for TMPK protein. Analyzing the Aurachin A and Soraphinol A binding, the established hydrogen bonds with Arg93 and the conserved hydrophobic interaction with Tyr101 are consistent with previous experimental interactions. Additionally, a deeper insight into the indole and the aromatic ring interaction through π-π stacking and π-cation interactions, as well as the background of Aurachin A and Soraphinol A as a bioactive compound, has significant implications not only for its potential as a promising drug but also for directing future drug discovery efforts targeting the TMPK protein.
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Affiliation(s)
- Yasir Ali
- Institute of Chemistry, Slovak Academy of Sciences, 845 38, Bratislava, Slovakia
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Amer M Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | | | - Junaid Ali Shah
- Ferghana Medical Institute of Public Health, 104100, Ferghana, Uzbekistan
| | - Zhi-Guang Ren
- Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University College of Medicine, Kaifeng, 475004, Henan, China.
| | - Saadullah Khattak
- Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University College of Medicine, Kaifeng, 475004, Henan, China.
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6
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Alagarsamy V, Shyam Sundar P, Raja Solomon V, Narendhar B, Sulthana MT, Rohitha K, Dhanwar S, Dharshini Aishwarya A, Murugesan S. Pharmacophore modelling-based drug repurposing approaches for monkeypox therapeutics. J Biomol Struct Dyn 2023; 41:10678-10689. [PMID: 36905675 DOI: 10.1080/07391102.2023.2188428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/05/2022] [Indexed: 03/13/2023]
Abstract
Monkeypox is a zoonotic viral disease that mainly affects tropical rainforest regions of central and west Africa, with sporadic exportations to other places. Since there is no cure, treating monkeypox with an antiviral drug developed for smallpox is currently acceptable. Our study mainly focused on finding new therapeutics to target monkeypox from existing compounds or medications. It is a successful method for discovering or developing medicinal compounds with novel pharmacological or therapeutic applications. In this study, homology modelling developed the Monkeypox VarTMPK (IMNR) structure. Ligand-based pharmacophore was generated using the best docking pose of standard ticovirimat. Further, molecular docking analysis showed compounds, tetrahydroxycurcumin, procyanidin, rutin, vicenin-2, kaempferol 3-(6''-malonylglucoside) were the top five binding energy compounds against VarTMPK (1MNR). Furthermore, we carried out MD simulations for 100 ns for the six compounds, including reference based on the binding energies and interactions. MD studies revealed that as ticovirimat interacted with residues Lys17, Ser18, and Arg45, all the above five compounds interacted with the same amino acids at the active site during docking and simulation studies. Among all the compounds, ZINC4649679 (Tetrahydroxycurcumin) was shown to have the highest binding energy -9.7 kcal/mol and also observed stable protein-ligand complex during MD studies. ADMET profile estimation showed that the docked phytochemicals were safe. However, further biological assessment through a wet lab is essential to measure the efficacy and safety of the compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- V Alagarsamy
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - P Shyam Sundar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - V Raja Solomon
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - B Narendhar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - M T Sulthana
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - Kotha Rohitha
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - Sangeeta Dhanwar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - A Dharshini Aishwarya
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - S Murugesan
- Department of Pharmacy, BITS, Pilani, Pilani, Rajasthan, India
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7
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Anderson GM, Anderson OE, Bosma CA, Brouwer EE, DeGroot KM, Hede OC, Jonouchi D, Kirkeby DJ, Klinghagen JT, Kralik KJ, Kutz JS, Lott OF, McKenney EJ, Pavik VL, Penner CH, Raymon G, Rozeboom LB, Skrien JL, Slight JK, Stokes MJ, Tiensvold JD, Wajer KJ, Trevino AL, Noordewier B, Tolsma SS. Complete genome sequences of microbacterium phages Tedro and BAjuniper. Microbiol Resour Announc 2023; 12:e0079323. [PMID: 37905824 PMCID: PMC10652889 DOI: 10.1128/mra.00793-23] [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: 08/24/2023] [Accepted: 09/27/2023] [Indexed: 11/02/2023] Open
Abstract
We purified two novel bacteriophages from soil collected in Sioux County, Iowa: BAjuniper and Tedro. These bacteriophages were isolated from the host, Microbacterium foliorum. BAjuniper was assigned to cluster EB, and Tedro was assigned to cluster EF. Both phages display genomes typical of other phages in their clusters.
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Affiliation(s)
| | | | - Clayton A. Bosma
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | - Erin E. Brouwer
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | | | - Owen C. Hede
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | - Daiki Jonouchi
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | - Dylan J. Kirkeby
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | | | - Kate J. Kralik
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | - Julia S. Kutz
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | - Olivia F. Lott
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | | | | | - Cayli H. Penner
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | - Garrett Raymon
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | - Leah B. Rozeboom
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | - Jett L. Skrien
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | | | - Maegan J. Stokes
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | | | - Kyra J. Wajer
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | | | - Byron Noordewier
- Department of Biology, Northwestern College, Orange City, Iowa, USA
| | - Sara S. Tolsma
- Department of Biology, Northwestern College, Orange City, Iowa, USA
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8
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Koirala S, Samanta S, Mahapatra S, Ursal KD, Poddar S, Kar P. Molecular level investigation for identifying potential inhibitors against thymidylate kinase of monkeypox through in silico approaches. J Biomol Struct Dyn 2023:1-14. [PMID: 37909473 DOI: 10.1080/07391102.2023.2274982] [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: 07/03/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
The need for more advanced and effective monkeypox (Mpox) treatments has become evident with numerous Mpox virus (MPXV) outbreaks. Over the years, interest has increased in developing targeted medicines that are efficient, safe, and precise while avoiding adverse effects. Here, we screened 32409 compounds against thymidylate kinase (TMPK), an emerging target for Mpox treatment. We studied their pharmacological characteristics and analyzed those through all-atom molecular dynamics simulations followed by molecular mechanics Poisson Boltzmann surface area (MM-PBSA) based free energy calculations. According to our findings, the leads CID40777874 and CID28960001 had the highest binding affinities towards TMPK with ΔGbind of -8.04 and -5.58 kcal/mol, respectively, which outperformed our control drug cidofovir (ΔGbind = -2.92 kcal/mol) in terms of binding favourability. Additionally, we observed crucial TMPK dynamics brought on by ligand-binding and identified key residues such as Phe68 and Tyr101 as the critical points of the protein-ligand interaction. The DCCM analysis revealed the role of ligand binding in stabilizing TMPK's binding region, as indicated by residual correlation motions. Moreover, the PSN analysis revealed that the interaction with ligand induces changes in residual network properties, enhancing the stability of complexes. We successfully identified novel compounds that may serve as potential building blocks for constructing contemporary antivirals against MPXV and highlighted the molecular mechanisms underlying their binding with TMPK. Overall, our findings will play a significant role in advancing the development of new therapies against Mpox and facilitating a comprehensive understanding of their interaction patterns.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suman Koirala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Sunanda Samanta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Subhasmita Mahapatra
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Kapil Dattatray Ursal
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Sayan Poddar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, MP, India
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9
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Wirth NT, Rohr K, Danchin A, Nikel PI. Recursive genome engineering decodes the evolutionary origin of an essential thymidylate kinase activity in Pseudomonas putida KT2440. mBio 2023; 14:e0108123. [PMID: 37732760 PMCID: PMC10653934 DOI: 10.1128/mbio.01081-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/27/2023] [Indexed: 09/22/2023] Open
Abstract
IMPORTANCE Investigating fundamental aspects of metabolism is vital for advancing our understanding of the diverse biochemical capabilities and biotechnological applications of bacteria. The origin of the essential thymidylate kinase function in the model bacterium Pseudomonas putida KT2440, seemingly interrupted due to the presence of a large genomic island that disrupts the cognate gene, eluded a satisfactory explanation thus far. This is a first-case example of an essential metabolic function, likely acquired by horizontal gene transfer, which "landed" in a locus encoding the same activity. As such, foreign DNA encoding an essential dNMPK could immediately adjust to the recipient host-instead of long-term accommodation and adaptation. Understanding how these functions evolve is a major biological question, and the work presented here is a decisive step toward this direction. Furthermore, identifying essential and accessory genes facilitates removing those deemed irrelevant in industrial settings-yielding genome-reduced cell factories with enhanced properties and genetic stability.
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Affiliation(s)
- Nicolas T. Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
| | - Katja Rohr
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
| | - Antoine Danchin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
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10
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Sahoo AK, Augusthian PD, Muralitharan I, Vivek-Ananth RP, Kumar K, Kumar G, Ranganathan G, Samal A. In silico identification of potential inhibitors of vital monkeypox virus proteins from FDA approved drugs. Mol Divers 2023; 27:2169-2184. [PMID: 36331784 PMCID: PMC9638297 DOI: 10.1007/s11030-022-10550-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
The World Health Organization (WHO) recently declared the monkeypox outbreak 'A public health emergency of international concern'. The monkeypox virus belongs to the same Orthopoxvirus genus as smallpox. Although smallpox drugs are recommended for use against monkeypox, monkeypox-specific drugs are not yet available. Drug repurposing is a viable and efficient approach in the face of such an outbreak. Therefore, we present a computational drug repurposing study to identify the existing approved drugs which can be potential inhibitors of vital monkeypox virus proteins, thymidylate kinase and D9 decapping enzyme. The target protein structures of the monkeypox virus were modelled using the corresponding protein structures in the vaccinia virus. We identified four potential inhibitors namely, Tipranavir, Cefiderocol, Doxorubicin, and Dolutegravir as candidates for repurposing against monkeypox virus from a library of US FDA approved antiviral and antibiotic drugs using molecular docking and molecular dynamics simulations. The main goal of this in silico study is to identify potential inhibitors against monkeypox virus proteins that can be further experimentally validated for the discovery of novel therapeutic agents against monkeypox disease.
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Affiliation(s)
- Ajaya Kumar Sahoo
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India
| | | | | | - R P Vivek-Ananth
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India
| | - Kishan Kumar
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
| | - Gaurav Kumar
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
| | | | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India.
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India.
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11
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Sib Tul Hassan Shah S, Naeem I. In-silico targeting TMPK from monkey pox virus: Molecular docking analysis, density functional theory studies and molecular dynamic simulation analysis. J Biomol Struct Dyn 2023; 41:14689-14701. [PMID: 36970852 DOI: 10.1080/07391102.2023.2193998] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/19/2023] [Indexed: 03/29/2023]
Abstract
The World Health Organization (WHO) proclaimed the monkeypox epidemic a "public health emergency of worldwide significance" recently. The monkeypox virus is a member of the same Orthopoxvirus genus as the smallpox virus. Although smallpox medications are advised against monkeypox, no monkeypox-specific drugs are currently available. In the event of such an outbreak, in-silico medication identification is a practical and efficient strategy. As a result, we report a computational drug repurposing analysis to discover medicines that may be potential inhibitors of thymidylate kinase, a critical monkeypox viral enzyme. The target protein structure of the monkeypox virus was modeled using the vaccinia virus's homologous protein structure. Using molecular docking and density functional theory, we found 11 possible inhibitors of the monkeypox virus from an Asinex library of 261120 chemicals. The primary purpose of this in silico work is to find possible inhibitors of monkeypox viral proteins that can then be experimentally tested in order to develop innovative therapeutic medicines for monkeypox infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Syed Sib Tul Hassan Shah
- Department of Life Science, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Iqra Naeem
- Department of Life Science, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
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12
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Barik K, Arya PK, Singh AK, Kumar A. Potential therapeutic targets for combating Mycoplasma genitalium. 3 Biotech 2023; 13:9. [PMID: 36532859 PMCID: PMC9755450 DOI: 10.1007/s13205-022-03423-9] [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: 06/22/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Mycoplasma genitalium (M. genitalium) has emerged as a sexually transmitted infection (STI) all over the world in the last three decades. It has been identified as a cause of male urethritis, and there is now evidence that it also causes cervicitis and pelvic inflammatory disease in women. However, the precise role of M. genitalium in diseases such as pelvic inflammatory disease, and infertility is unknown, and more research is required. It is a slow-growing organism, and with the advent of the nucleic acid amplification test (NAAT), more studies are being conducted and knowledge about the pathogenicity of this organism is being elucidated. The accumulation of data has improved our understanding of the pathogen and its role in disease transmission. Despite the widespread use of single-dose azithromycin in the sexual health field, M. genitalium is known to rapidly develop antibiotic resistance. As a result, the media frequently refer to this pathogen as the "new STI superbug." Despite their rarity, antibiotics available today have serious side effects. As the cure rates for first-line antimicrobials have decreased, it is now a challenge to determine the effective antimicrobial therapy. In this review, we summarise recent M. genitalium research and investigate potential therapeutic targets for combating this pathogen.
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Affiliation(s)
- Krishnendu Barik
- Department of Bioinformatics, Central University of South Bihar, Gaya, 824236 India
| | - Praffulla Kumar Arya
- Department of Bioinformatics, Central University of South Bihar, Gaya, 824236 India
| | - Ajay Kumar Singh
- Department of Bioinformatics, Central University of South Bihar, Gaya, 824236 India
| | - Anil Kumar
- Department of Bioinformatics, Central University of South Bihar, Gaya, 824236 India
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13
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Habib MR, Hamed AA, Ali REM, Zayed KM, Gad El-Karim RM, Sabour R, Abu El-Einin HM, Ghareeb MA. Thais savignyi tissue extract: bioactivity, chemical composition, and molecular docking. PHARMACEUTICAL BIOLOGY 2022; 60:1899-1914. [PMID: 36200747 PMCID: PMC9553184 DOI: 10.1080/13880209.2022.2123940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 08/15/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
CONTEXT Thais savignyi Deshayes (Muricidae) is widely distributed in the Red Sea. Its abundance and the history of Muricidae in traditional medicine make it a tempting target for investigation. OBJECTIVE To investigate the chemical profile and biological activities of T. savignyi tissue extracts. MATERIALS AND METHODS Methanol, ethanol, acetone, and ethyl acetate extracts from T. savignyi tissue were compared in their antioxidant by total antioxidant capacity, DPPH free radical scavenging, and total phenolic content. In addition, the antimicrobial, and antibiofilm properties (at 250 µg/mL) of the extracts were tested against Escherichia coli, Pseudomonas aeruginosa, Proteus vulgaris, Klebsiella pneumoniae, Staphylococcus aureus, and Candida albicans. The antioxidant extract with greatest activity was assessed for cytotoxicity (range 0.4-100 µg/mL) against 3 human cancer cell lines (UO-31, A549 and A431), and its chemical composition was investigated using GC-MS. Moreover, docking simulation was performed to predict its constituents' binding modes/scores to the active sites of thymidylate kinase. RESULTS The ethyl acetate extract (Ts-EtOAc) showed the highest total antioxidant capacity (551.33 mg AAE/g dry weight), total phenolics (254.46 mg GAE/g dry weight), and DPPH scavenging (IC50= 24.0 µg/mL). Ts-EtOAc exhibited strong antibacterial (MIC: 3.9 µg/mL against K. pneumoniae), antibiofilm (MIC: 7.81 µg/mL against S. aureus), and antifungal (MIC: 3.9 µg/mL against C. albicans) activities and considerable cytotoxicity against cancer cells (UO-31: IC50= 19.96 ± 0.93, A549: IC50= 25.04 ± 1.15 μg/mL). GC-MS identified multiple bioactive metabolites in Ts-EtOAc extract belonging to miscellaneous chemical classes. Molecular docking studies revealed that the constituents of Ts-EtOAc have antibacterial potential. DISCUSSION AND CONCLUSIONS T. savignyi extract has considerable antimicrobial and cytotoxic activities. Further studies are needed to isolate the active constituents of this snail for comprehensive drug discovery tests.
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Affiliation(s)
- Mohamed R. Habib
- Medical Malacology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Ahmed A. Hamed
- Microbial Chemistry Department, National Research Center, Giza, Egypt
| | - Rasha E. M. Ali
- Medical Malacology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Khaled M. Zayed
- Medical Malacology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | | | - Rehab Sabour
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | | | - Mosad A. Ghareeb
- Medicinal Chemistry Department, Theodor Bilharz Research Institute, Giza, Egypt
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14
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Lan T, Wang Y, Miao J, Guo H, Wang Z, Wang J, Zhang C, Yang P, Zhang Z, Dunmall LC, Wang Y. Deoxythymidylate Kinase as a Promising Marker for Predicting Prognosis and Immune Cell Infiltration of Pan-cancer. Front Mol Biosci 2022; 9:887059. [PMID: 35903153 PMCID: PMC9315941 DOI: 10.3389/fmolb.2022.887059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Deoxythymidylate kinase (DTYMK) serves as a pyrimidine metabolic rate-limiting enzyme that catalyzes deoxythymidine monophosphate (dTMP) to generate deoxythymidine diphosphate (dTDP). It remains unclear whether DTYMK expression has the potential to predict outcome and immune cell infiltration in cancers. Methods: DTYMK expression profile was analyzed using Oncomine, TIMER, GEPIA and UALCAN databases. The influence of DTYMK on immune infiltration was examined using TIMER and TISIDB databases. DTYMK interactive gene hub and co-expressing genes were obtained and analyzed by STRING and Linkedomics, respectively. The relationship between DTYMK expression and patient prognosis was validated using GEPIA, Kaplan-Meier plotter, and PrognoScan databases. The functions of DTYMK in cancer cells were also biologically validated in vitro. Results: DTYMK expression was elevated in tumor tissues compared with their control counterparts. DTYMK expression varied in different stages and discriminatorily distributed in different immune and molecular subtypes. Higher expression of DTYMK predicted worse outcome in several cancer types such as liver hepatocellular carcinoma (LIHC) and lung adenocarcinoma (LUAD). High DTYMK expression was positively or negatively correlated with immune cell infiltration, including B cell, CD8+ cell, CD4+ T cell, macrophage, neutrophil and dendritic cell, depending on the type of cancers. Additionally, DTYMK co-expressing genes participated in pyrimidine metabolism as well as in T helper cell differentiation in LIHC and LUAD. In vitro, knockdown of DTYMK suppressed cell migration of liver and lung cancer cells. Conclusion: DTYMK might be taken as an useful prognostic and immunological marker in cancers and further investigation is warrented.
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Affiliation(s)
- Tianfeng Lan
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Sino-British Research Center for Molecular Oncology, National Center for the International Research in Cell and Gene Therapy, School of Basic Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yachao Wang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Sino-British Research Center for Molecular Oncology, National Center for the International Research in Cell and Gene Therapy, School of Basic Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jinxin Miao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Sino-British Research Center for Molecular Oncology, National Center for the International Research in Cell and Gene Therapy, School of Basic Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Academy of Chinese Medicine Science, Henan University of Chinese Medicine, Zhengzhou, China
| | - Haoran Guo
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Sino-British Research Center for Molecular Oncology, National Center for the International Research in Cell and Gene Therapy, School of Basic Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zheng Wang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Sino-British Research Center for Molecular Oncology, National Center for the International Research in Cell and Gene Therapy, School of Basic Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jianyao Wang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Sino-British Research Center for Molecular Oncology, National Center for the International Research in Cell and Gene Therapy, School of Basic Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Chunyang Zhang
- Department of Surgical Sciences, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Panpan Yang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Sino-British Research Center for Molecular Oncology, National Center for the International Research in Cell and Gene Therapy, School of Basic Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhongxian Zhang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Sino-British Research Center for Molecular Oncology, National Center for the International Research in Cell and Gene Therapy, School of Basic Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Louisa Chard Dunmall
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Yaohe Wang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Sino-British Research Center for Molecular Oncology, National Center for the International Research in Cell and Gene Therapy, School of Basic Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
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15
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Dual transcriptome based reconstruction of Salmonella-human integrated metabolic network to screen potential drug targets. PLoS One 2022; 17:e0268889. [PMID: 35609089 PMCID: PMC9129043 DOI: 10.1371/journal.pone.0268889] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/10/2022] [Indexed: 11/19/2022] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a highly adaptive pathogenic bacteria with a serious public health concern due to its increasing resistance to antibiotics. Therefore, identification of novel drug targets for S. Typhimurium is crucial. Here, we first created a pathogen-host integrated genome-scale metabolic network by combining the metabolic models of human and S. Typhimurium, which we further tailored to the pathogenic state by the integration of dual transcriptome data. The integrated metabolic model enabled simultaneous investigation of metabolic alterations in human cells and S. Typhimurium during infection. Then, we used the tailored pathogen-host integrated genome-scale metabolic network to predict essential genes in the pathogen, which are candidate novel drug targets to inhibit infection. Drug target prioritization procedure was applied to these targets, and pabB was chosen as a putative drug target. It has an essential role in 4-aminobenzoic acid (PABA) synthesis, which is an essential biomolecule for many pathogens. A structure based virtual screening was applied through docking simulations to predict candidate compounds that eliminate S. Typhimurium infection by inhibiting pabB. To our knowledge, this is the first comprehensive study for predicting drug targets and drug like molecules by using pathogen-host integrated genome-scale models, dual RNA-seq data and structure-based virtual screening protocols. This framework will be useful in proposing novel drug targets and drugs for antibiotic-resistant pathogens.
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16
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Ramesh D, Sarkar D, Joji A, Singh M, Mohanty AK, G Vijayakumar B, Chatterjee M, Sriram D, Muthuvel SK, Kannan T. First-in-class pyrido[2,3-d]pyrimidine-2,4(1H,3H)-diones against leishmaniasis and tuberculosis: Rationale, in vitro, ex vivo studies and mechanistic insights. Arch Pharm (Weinheim) 2022; 355:e2100440. [PMID: 35106845 DOI: 10.1002/ardp.202100440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/22/2021] [Accepted: 01/07/2022] [Indexed: 11/06/2022]
Abstract
Pyrido[2,3-d]pyrimidine-2,4(1H,3H)-diones were synthesized, for the first time, from indole chalcones and 6-aminouracil, and their ability to inhibit leishmaniasis and tuberculosis (Tb) infections was evaluated. The in vitro antileishmanial activity against promastigotes of Leishmania donovani revealed exceptional activities of compounds 3, 12 and 13, with IC50 values ranging from 10.23 ± 1.50 to 15.58 ± 1.67 µg/ml, which is better than the IC50 value of the standard drug pentostam of 500 μg/ml. The selectivity of the compounds towards Leishmania parasites was evaluated via ex vivo studies in Swiss albino mice. The efficiency of these compounds against Tb infection was then evaluated using the in vitro anti-Tb microplate Alamar Blue assay. Five compounds, 3, 7, 8, 9 and 12, showed MIC100 values against the Mycobacterium tuberculosis H37 Rv strain at 25 µg/ml, and compound 20 yielded an MIC100 value of 50 µg/ml. Molecular modelling of these compounds highlighted interactions with binding sites of dihydrofolate reductase, pteridine reductase and thymidylate kinase, thus establishing the rationale of their pharmacological activity against both pathogens, which is consistent with the in vitro results. From the above results, it is clear that compounds 3 and 12 are promising lead candidates for Leishmania and Mycobacterium infections and may be promising for coinfections.
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Affiliation(s)
- Deepthi Ramesh
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry, India
| | - Deblina Sarkar
- Department of Pharmacology, Institute of Post Graduate Medical Education & Research (IPGME&R), Kolkata, West Bengal, India
| | - Annu Joji
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry, India
| | - Monica Singh
- Department of Pharmacy, Birla Institute of Technology & Science Pilani, Hyderabad, India
| | - Amaresh K Mohanty
- Department of Bioinformatics, Pondicherry University, Kalapet, Puducherry, India
| | | | - Mitali Chatterjee
- Department of Pharmacology, Institute of Post Graduate Medical Education & Research (IPGME&R), Kolkata, West Bengal, India
| | - Dharmarajan Sriram
- Department of Pharmacy, Birla Institute of Technology & Science Pilani, Hyderabad, India
| | - Suresh K Muthuvel
- Department of Bioinformatics, Pondicherry University, Kalapet, Puducherry, India
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17
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Blindheim FH, Malme AT, Dalhus B, Sundby E, Hoff BH. Synthesis and Evaluation of Fused Pyrimidines
as E. coli
Thymidylate Monophosphate Kinase Inhibitors. ChemistrySelect 2021. [DOI: 10.1002/slct.202103796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Fredrik Heen Blindheim
- Department of Chemistry Norwegian University of Science and Technology (NTNU) Høgskoleringen 5 NO-7491 Trondheim Norway
| | - Ane Thoresen Malme
- Department of Chemistry Norwegian University of Science and Technology (NTNU) Høgskoleringen 5 NO-7491 Trondheim Norway
- BASF AS Framnesveien 41 3222 Sandefjord Norway
| | - Bjørn Dalhus
- Department of Medical Biochemistry University of Oslo and Department for Microbiology Oslo University Hospital Rikshospitalet, Postbox 4950, Nydalen 0424 Oslo Norway
| | - Eirik Sundby
- Department of Material Science Norwegian University of Science and Technology (NTNU) Høgskoleringen 5 NO-7491 Trondheim Norway
| | - Bård Helge Hoff
- Department of Chemistry Norwegian University of Science and Technology (NTNU) Høgskoleringen 5 NO-7491 Trondheim Norway
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18
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Garcia DR, Souza FR, Guimarães AP, Valis M, Pavelek Z, Kuca K, Ramalho TC, França TCC. In Silico Studies of Potential Selective Inhibitors of Thymidylate Kinase from Variola virus. Pharmaceuticals (Basel) 2021; 14:ph14101027. [PMID: 34681251 PMCID: PMC8537287 DOI: 10.3390/ph14101027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 11/17/2022] Open
Abstract
Continuing the work developed by our research group, in the present manuscript, we performed a theoretical study of 10 new structures derived from the antivirals cidofovir and ribavirin, as inhibitor prototypes for the enzyme thymidylate kinase from Variola virus (VarTMPK). The proposed structures were subjected to docking calculations, molecular dynamics simulations, and free energy calculations, using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method, inside the active sites of VarTMPK and human TMPK (HssTMPK). The docking and molecular dynamic studies pointed to structures 2, 3, 4, 6, and 9 as more selective towards VarTMPK. In addition, the free energy data calculated through the MM-PBSA method, corroborated these results. This suggests that these compounds are potential selective inhibitors of VarTMPK and, thus, can be considered as template molecules to be synthesized and experimentally evaluated against smallpox.
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Affiliation(s)
- Danielle R. Garcia
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Praça General Tiburcio 80, Urca, Rio de Janeiro 22290-270, Brazil;
| | - Felipe R. Souza
- Department of Chemistry, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro 22541-041, Brazil;
| | - Ana P. Guimarães
- Department of Chemistry, Federal University of Viçosa, Avenida P. H. Rolfs, s/n, Centro, Viçosa 36570-000, MG, Brazil;
| | - Martin Valis
- Department of Neurology of the Medical Faculty of Charles University and University Hospital in Hradec Kralove, Sokolska 581, 50005 Hradec Kralove, Czech Republic; (M.V.); (Z.P.)
| | - Zbyšek Pavelek
- Department of Neurology of the Medical Faculty of Charles University and University Hospital in Hradec Kralove, Sokolska 581, 50005 Hradec Kralove, Czech Republic; (M.V.); (Z.P.)
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003 Hradec Kralove, Czech Republic;
- Biomedical Research Center, University Hospital in Hradec Kralove, Sokolska 581, 50005 Hradec Kralove, Czech Republic
- Correspondence: (K.K.); (T.C.C.F.)
| | - Teodorico C. Ramalho
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003 Hradec Kralove, Czech Republic;
- Laboratory of Computational Chemistry, Department of Chemistry, UFLA, Lavras 37200-000, MG, Brazil
| | - Tanos C. C. França
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Praça General Tiburcio 80, Urca, Rio de Janeiro 22290-270, Brazil;
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 50003 Hradec Kralove, Czech Republic;
- Correspondence: (K.K.); (T.C.C.F.)
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Kirti A, Prashar V, Kumar A, Pandey S, Rajaram H. Thymidylate kinase (TMK) of the photosynthetic, nitrogen-fixing cyanobacterium Nostoc sp. strain PCC7120: Biophysical, biochemical and physiological characterisation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:416-426. [PMID: 34157604 DOI: 10.1016/j.plaphy.2021.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Thymidylate kinase (TMK/TMPK) is an important enzyme in DNA biosynthesis and catalyses the conversion of dTMP to dTDP. Due to its therapeutic potential, the focus has been on characterizing the TMK proteins of pathogens and human origin, with very little information available on the TMK proteins of photosynthetic organisms and agriculturally important nitrogen-fixing organisms. In this work we report the characterisation of TMK in an evolutionarily ancient organism, cyanobacteria. The TMK protein of the photosynthetic, nitrogen-fixing cyanobacterium Nostoc PCC7120 (AnTMK) was found to have low conformational stability, which related to its low Tm of ~46 °C confirmed by Differential Scanning Fluorimetry (DSF) and Differential Scanning Calorimetry (DSC) techniques. The AnTMK protein exhibited substrate specificity for dTMP and ATP with Km of 20.74 ± 1.47 μM and 20.17 ± 2.96 μM respectively. The enzyme kinetics data and the positive co-operativity observed between dTMP and ATP binding correlated well with the data obtained from Isothermal Titration Calorimetry (ITC). Homology model of the enzyme suggested that the binding mode of substrate nucleotides to the enzyme is conserved. When overexpressed constitutively in Nostoc PCC7120 (Antmk+), it supported faster growth measured in terms of chlorophyll a content under normal growth conditions, but exhibited lower photosynthetic efficiency. Compared to the vector control recombinant Nostoc AnpAM, the Antmk + cells exhibited higher photoinhibition at higher light irradiance with more open reaction centres and lower dissipation of heat, indicative of damage to photosynthetic machinery. This indicated that the TMK is likely to have a significant role in photosynthetic organisms.
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Affiliation(s)
- Anurag Kirti
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Vishal Prashar
- Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India.
| | - Arvind Kumar
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Sarita Pandey
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Hema Rajaram
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India.
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20
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Blindheim FH, Olsen CE, Krogh Søgaard C, Otterlei M, Sundby E, Hoff BH. Synthetic Strategies towards Imidazopyridinones and 7‐Azaoxindoles and their Evaluation as Antibacterial Agents. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fredrik Heen Blindheim
- Department of Chemistry Norwegian University of Science and Technology (NTNU) 7491 Trondheim Norway
| | - Cecilie Elisabeth Olsen
- Department of Chemistry Norwegian University of Science and Technology (NTNU) 7491 Trondheim Norway
| | - Caroline Krogh Søgaard
- Department of Clinical and Molecular Medicine Norwegian University of Science and Technology (NTNU) 7489 Trondheim Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine Norwegian University of Science and Technology (NTNU) 7489 Trondheim Norway
| | - Eirik Sundby
- Department of Material Science Norwegian University of Science and Technology (NTNU) 7491 Trondheim Norway
| | - Bård Helge Hoff
- Department of Chemistry Norwegian University of Science and Technology (NTNU) 7491 Trondheim Norway
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21
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Chen T, Xiong H, Yang JF, Zhu XL, Qu RY, Yang GF. Diaryl Ether: A Privileged Scaffold for Drug and Agrochemical Discovery. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9839-9877. [PMID: 32786826 DOI: 10.1021/acs.jafc.0c03369] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Diaryl ether (DE) is a functional scaffold existing widely both in natural products (NPs) and synthetic organic compounds. Statistically, DE is the second most popular and enduring scaffold within the numerous medicinal chemistry and agrochemical reports. Given its unique physicochemical properties and potential biological activities, DE nucleus is recognized as a fundamental element of medicinal and agrochemical agents aimed at different biological targets. Its drug-like derivatives have been extensively synthesized with interesting biological features including anticancer, anti-inflammatory, antiviral, antibacterial, antimalarial, herbicidal, fungicidal, insecticidal, and so on. In this review, we highlight the medicinal and agrochemical versatility of the DE motif according to the published information in the past decade and comprehensively give a summary of the target recognition, structure-activity relationship (SAR), and mechanism of action of its analogues. It is expected that this profile may provide valuable guidance for the discovery of new active ingredients both in drug and pesticide research.
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Affiliation(s)
- Tao Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Hao Xiong
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Ren-Yu Qu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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Frisk JH, Eriksson S, Pejler G, Wang L. Identification of a novel thymidylate kinase activity. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:1359-1368. [PMID: 32345121 DOI: 10.1080/15257770.2020.1755043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Thymidylate kinase (TMPK, EC2.7.4.9) is the enzyme that converts deoxythymidine monophosphate (dTMP) to deoxythymidine diphosphate (dTDP) in the synthesis of dTTP, an essential building block of DNA. To date, there is only one gene (TYMK) known to encode TMPK in mammalian cells. In this study, we investigated the distribution of TMPK activity and protein in subcellular fractions by using activity measurements and by using a specific antibody against TYMK-encoded TMPK (canonical TMPK). TMPK activity was detected in all subcellular fractions, of which the mitochondrial outer membrane contained the highest activity. High levels of canonical TMPK protein were detected in the cytosolic fraction, whereas low levels were found in the nuclear and mitochondrial matrix fractions. Strikingly, despite the detection of high TMPK activity in the mitochondrial outer membrane, canonical TMPK protein was not detected in this fraction. These results suggest that the TMPK activity detected in the outer membrane fraction may originate from a novel dTMP kinase, distinct from the canonical TYMK.
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Affiliation(s)
- Junmei Hu Frisk
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Staffan Eriksson
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gunnar Pejler
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Liya Wang
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
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23
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Gul S, Khalil R, Zaheer Ul-Haq, Mubarak MS. Computational Overview of Mycobacterial Thymidine Monophosphate Kinase. Curr Pharm Des 2020; 26:1676-1681. [PMID: 32242781 DOI: 10.2174/1381612826666200403114152] [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: 10/04/2019] [Accepted: 12/30/2019] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) ranks among the diseases with the highest morbidity rate with significantly high prevalence in developing countries. Globally, tuberculosis poses the most substantial burden of mortality. Further, a partially treated tuberculosis patient is worse than untreated; they may lead to standing out as a critical obstacle to global tuberculosis control. The emergence of multi-drug resistant (MDR) and extremely drug-resistant (XDR) strains, and co-infection of HIV further worsen the situation. The present review article discusses validated targets of the bacterial enzyme thymidine monophosphate kinase (TMPK). TMPKMTB enzyme belongs to the nucleoside monophosphate kinases (NMPKs) family. It is involved in phosphorylation of TMP to TDP, and TDP is phosphorylated to TTP. This review highlights structure elucidation of TMP enzymes and their inhibitors study on TMP scaffold, and it also discusses different techniques; including molecular docking, virtual screening, 3DPharmacophore, QSAR for finding anti-tubercular agents.
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Affiliation(s)
- Sana Gul
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi-75210, Pakistan
| | - Ruqaiya Khalil
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi-75210, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi-75210, Pakistan
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24
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Fucci IJ, Sinha K, Rule GS. Stabilization of Active Site Dynamics Leads to Increased Activity with 3'-Azido-3'-deoxythymidine Monophosphate for F105Y Mutant Human Thymidylate Kinase. ACS OMEGA 2020; 5:2355-2367. [PMID: 32064397 PMCID: PMC7017412 DOI: 10.1021/acsomega.9b03766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/10/2020] [Indexed: 05/04/2023]
Abstract
Thymidylate kinases are essential enzymes with roles in DNA synthesis and repair and have been the target of drug development for antimalarials, antifungals, HIV treatment, and cancer therapeutics. Human thymidylate kinase (hTMPK) conversion of the anti-HIV prodrug 3'-azido-3'-deoxythymidine (AZT or zidovudine) monophosphate to diphosphate is the rate-limiting step in the activation of AZT. A point mutant (F105Y) has been previously reported with significantly increased activity for the monophosphate form of the drug [3'-azidothymidine-5'-monophosphate (AZTMP)]. Using solution nuclear magnetic resonance (NMR) techniques, we show that while the wild-type (WT) and F105Y hTMPK adopt the same structure in solution, significant changes in dynamics may explain their different activities toward TMP and AZTMP. 13C spin-relaxation measurements show that there is little change in dynamics on the ps to ns time scale. In contrast, methyl 1H relaxation dispersion shows that AZTMP alters adenosine nucleotide handling in the WT protein but not in the mutant. Additionally, the F105Y mutant has reduced conformational flexibility, leading to an increase in affinity for the product ADP and a slower rate of phosphorylation of TMP. The dynamics at the catalytic center for F105Y bound to AZTMP are tuned to the same frequency as WT bound to TMP, which may explain the mutant's catalytic efficiency toward the prodrug.
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25
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Sardar S, Wilfred CD, Mumtaz A, Leveque JM, Kalsoom S, Gonfa G. Cytoxicity, Hammett acidity and CO2 solubility of AMPS-based organic salts: A comparative analysis of experimental and computational tools. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Chen MD, Fucci IJ, Sinha K, Rule GS. dGMP Binding to Thymidylate Kinase from Plasmodium falciparum Shows Half-Site Binding and Induces Protein Dynamics at the Dimer Interface. Biochemistry 2020; 59:694-703. [PMID: 31934749 DOI: 10.1021/acs.biochem.9b00898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plasmodium falciparum thymidylate kinase (PfTMK) is an essential enzyme for the growth of the organism because of its critical role in the de novo synthesis of deoxythymidine 5'-diphosphate (TDP), a precursor for TTP that is required for DNA replication and repair. The kinetics, thermodynamic parameters, and substrate binding properties of PfTMK for TMP, dGMP, ADP, and ATP were measured and characterized by steady-state kinetics and a combination of isothermal titration calorimetry, tryptophan fluorescence titration, and NMR. Mutational studies were performed to investigate residues that contribute to the unique ability of PfTMK to also utilize dGMP as a substrate. Isothermal titration calorimetry experiments revealed that dGMP binding exhibits a unique half-site binding mechanism. The occlusion of the empty site in the dGMP complex is supported by molecular mechanics calculations. Relaxation dispersion experiments show that the dGMP and enzyme complex is more dynamic at the dimer interface than the TMP complex on the μs-ms time scale. The unique properties of dGMP binding need to be considered in the design of guanosine-based PfTMK-specific inhibitors.
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Affiliation(s)
- Mengshen David Chen
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Ian J Fucci
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Kaustubh Sinha
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Gordon S Rule
- Department of Biological Sciences , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
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27
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Jian Y, Risseeuw MDP, Froeyen M, Song L, Cappoen D, Cos P, Munier-Lehmann H, van Calenbergh S. 1-(Piperidin-3-yl)thymine amides as inhibitors of M. tuberculosis thymidylate kinase. J Enzyme Inhib Med Chem 2019; 34:1730-1739. [PMID: 31822127 PMCID: PMC6920704 DOI: 10.1080/14756366.2019.1662790] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A series of readily accessible 1-(piperidin-3-yl)thymine amides was designed, synthesised and evaluated as Mycobacterium tuberculosis TMPK (MtbTMPK) inhibitors. In line with the modelling results, most inhibitors showed reasonable MtbTMPK inhibitory activity. Compounds 4b and 4i were slightly more potent than the parent compound 3. Moreover, contrary to the latter, amide analogue 4g was active against the avirulent M. tuberculosis H37Ra strain (MIC50=35 µM). This finding opens avenues for future modifications.
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Affiliation(s)
- Yanlin Jian
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Martijn D P Risseeuw
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Mathy Froeyen
- Department of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Lijun Song
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Davie Cappoen
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Paul Cos
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Hélène Munier-Lehmann
- Unit of Chemistry and Biocatalysis, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, Paris, France
| | - Serge van Calenbergh
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
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28
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Hussain M, Qadri T, Hussain Z, Saeed A, Channar PA, Shehzadi SA, Hassan M, Larik FA, Mahmood T, Malik A. Synthesis, antibacterial activity and molecular docking study of vanillin derived 1,4-disubstituted 1,2,3-triazoles as inhibitors of bacterial DNA synthesis. Heliyon 2019; 5:e02812. [PMID: 31768438 PMCID: PMC6872831 DOI: 10.1016/j.heliyon.2019.e02812] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/13/2019] [Accepted: 11/07/2019] [Indexed: 01/03/2023] Open
Abstract
Antimicrobial resistance (AMR) compelled scientists in general while pharmacists, chemists and biologists in specific to believe that we could always remain ahead of the pathogens. The pipeline of new drugs is running gasping and the inducements to develop new antimicrobials to address the global problems of drug resistance are weak. In this pursuit, effective endeavours to prepare new anti-bacterial entities is highly wished. The present study demonstrates successful synthesis of a library of 1,4-disbustituted 1,2,3-triazoles (3a-3k) using Click-chemistry concept and anti-their bacterial potential. In this 1,3-dipolar cycloaddition, the 3-methoxy-4-(prop-2-yn-1-yloxy)benzaldehyde (1) was used as alkyne partner which was synthesized from vanillin and propargyl bromide and further reacted with differently substituted arylpropoxy azides (2a-k) to furnish series of mono and bis1,4-disubstituted-1,2,3-triazoles. All the synthesized compounds were characterized spectroscopically and were evaluated for their initial antimicrobial activity. Preliminary results of antibacterial screening revealed that the synthesized compounds have the highest inhibitory effects compare to the control ciprofloxacin. The compounds 3b and 3g were found to be the most active (MIC: 5 μg/mL, MIC: 10 μg/mL respectively) against various strains of gram-positive and gram-negative bacteria. The molecular docking study against 4GQQ protein with synthesized ligands was performed to see the necessary interactions responsible for anti-bacterial activity. The docking analysis of the most potent compound 3g supported the antibacterial activity exhibiting high inhibition constant and binding energy.
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Affiliation(s)
- Mumtaz Hussain
- Department of Chemistry, University of Karachi, 75270, Karachi, Pakistan
| | - Tahir Qadri
- Department of Chemistry, University of Karachi, 75270, Karachi, Pakistan
| | - Zahid Hussain
- Department of Chemistry, University of Karachi, 75270, Karachi, Pakistan
| | - Aamer Saeed
- Department of Chemistry, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - Pervaiz Ali Channar
- Department of Chemistry, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - Syeda Aaliya Shehzadi
- Sulaiman Bin Abdullah Aba Al-Khail-Centre for Interdisciplinary Research in Basic Sciences (SA-CIRBS), International Islamic University, 44000, Islamabad, Pakistan
| | - Mubashir Hassan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Defence Road Campus, Lahore, Pakistan
| | - Fayaz Ali Larik
- Department of Chemistry, Quaid-i-Azam University, 45320, Islamabad, Pakistan
| | - Tarique Mahmood
- Department of Chemistry, University of Karachi, 75270, Karachi, Pakistan
| | - Arif Malik
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Defence Road Campus, Lahore, Pakistan
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29
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Sharma R, Pielstick BA, Bell KA, Nieman TB, Stubbs OA, Yeates EL, Baltrus DA, Grose JH. A Novel, Highly Related Jumbo Family of Bacteriophages That Were Isolated Against Erwinia. Front Microbiol 2019; 10:1533. [PMID: 31428059 PMCID: PMC6690015 DOI: 10.3389/fmicb.2019.01533] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/19/2019] [Indexed: 01/17/2023] Open
Abstract
Erwinia amylovora is a plant pathogen from the Erwiniaceae family and a causative agent of the devastating agricultural disease fire blight. Here we characterize eight lytic bacteriophages of E. amylovora that we isolated from the Wasatch front (Utah, United States) that are highly similar to vB_EamM_Ea35-70 which was isolated in Ontario, Canada. With the genome size ranging from 271 to 275 kb, this is a novel jumbo family of bacteriophages. These jumbo bacteriophages were further characterized through genomic and proteomic comparison, mass spectrometry, host range and burst size. Their proteomes are highly unstudied, with over 200 putative proteins with no known homologs. The production of 27 of these putative proteins was confirmed by mass spectrometry analysis. These bacteriophages appear to be most similar to bacteriophages that infect Pseudomonas and Ralstonia rather than Enterobacteriales bacteria by protein similarity, however, we were only able to detect infection of Erwinia and the closely related strains of Pantoea.
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Affiliation(s)
- Ruchira Sharma
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Brittany A. Pielstick
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Kimberly A. Bell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Tanner B. Nieman
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Olivia A. Stubbs
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Edward L. Yeates
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - David A. Baltrus
- School of Plant Sciences, The University of Arizona, Tucson, AZ, United States
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
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30
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Huang CY, Chen YC, Wu-Hsieh BA, Fang JM, Chang ZF. The Ca-loop in thymidylate kinase is critical for growth and contributes to pyrimidine drug sensitivity of Candida albicans. J Biol Chem 2019; 294:10686-10697. [PMID: 31152062 DOI: 10.1074/jbc.ra118.006798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 05/29/2019] [Indexed: 11/06/2022] Open
Abstract
The yeast Candida albicans is the most prevalent opportunistic fungal pathogen in humans. Drug resistance among C. albicans isolates poses a common challenge, and overcoming this resistance represents an unmet need in managing this common pathogen. Here, we investigated CDC8, encoding thymidylate kinase (TMPK), as a potential drug target for the management of C. albicans infections. We found that the region spanning amino acids 106-123, namely the Ca-loop of C. albicans TMPK (CaTMPK), contributes to the hyperactivity of this enzyme compared with the human enzyme (hTMPK) and to the utilization of deoxyuridine monophosphate (dUMP)/deoxy-5-fluorouridine monophosphate (5-FdUMP) as a substrate. Notably, expression of CaTMPK, but not of hTMPK, produced dUTP/5-FdUTP-mediated DNA toxicity in budding yeast (Saccharomyces cerevisiae). CRISPR-mediated deletion of this Ca-loop in C. albicans revealed that the Ca-loop is critical for fungal growth and susceptibility to 5-fluorouridine (5-FUrd). Of note, pathogenic and drug-resistant C. albicans clones were similarly sensitive to 5-FUrd, and we also found that CaTMPK is essential for the growth of C. albicans In conclusion, these findings not only identified a target site for the development of CaTMPK-selective drugs, but also revealed that 5-FUrd may have potential utility as drug for managing C. albicans infections.
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Affiliation(s)
- Chang-Yu Huang
- From the Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Linong Street, Taipei 11221.,the Institute of Molecular Medicine, College of Medicine, National Taiwan University, Jen-Ai Road, Taipei 10051
| | - Yee-Chun Chen
- the National Taiwan University Hospital and College of Medicine.,Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002
| | - Betty A Wu-Hsieh
- the Graduate Institute of Immunology, College of Medicine, National Taiwan University, Jen-Ai Road, Taipei 10051, and
| | - Jim-Min Fang
- the Department of Chemistry, National Taiwan University, Taipei City 10617, Taiwan
| | - Zee-Fen Chang
- From the Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Linong Street, Taipei 11221, .,the Institute of Molecular Medicine, College of Medicine, National Taiwan University, Jen-Ai Road, Taipei 10051.,Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002
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31
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Gautam LK, Sharma P, Capalash N. Bacterial Polyphosphate Kinases Revisited: Role in Pathogenesis and Therapeutic Potential. Curr Drug Targets 2019; 20:292-301. [DOI: 10.2174/1389450119666180801120231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/02/2018] [Accepted: 07/31/2018] [Indexed: 11/22/2022]
Abstract
Bacterial infections have always been an unrestrained challenge to the medical community due to the rise of multi-drug tolerant and resistant strains. Pioneering work on Escherichia coli polyphosphate kinase (PPK) by Arthur Kornberg has generated great interest in this polyphosphate (PolyP) synthesizing enzyme. PPK has wide distribution among pathogens and is involved in promoting pathogenesis, stress management and susceptibility to antibiotics. Further, the absence of a PPK orthologue in humans makes it a potential drug target. This review covers the functional and structural aspects of polyphosphate kinases in bacterial pathogens. A description of molecules being designed against PPKs has been provided, challenges associated with PPK inhibitor design are highlighted and the strategies to enable development of efficient drug against this enzyme have also been discussed.
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Affiliation(s)
- Lalit Kumar Gautam
- Department of Biotechnology, Panjab University, BMS Block-I, Sector- 25, Chandigarh, 160014, India
| | - Prince Sharma
- Department of Microbiology, Panjab University, BMS Block-I, Sector- 25, Chandigarh, 160014, India
| | - Neena Capalash
- Department of Biotechnology, Panjab University, BMS Block-I, Sector- 25, Chandigarh, 160014, India
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32
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Lopez-Zavala AA, Guevara-Hernandez E, Vazquez-Lujan LH, Sanchez-Paz A, Garcia-Orozco KD, Contreras-Vergara CA, Lopez-Leal G, Arvizu-Flores AA, Ochoa-Leyva A, Sotelo-Mundo RR. A novel thymidylate synthase from the Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP) clade with altered nucleotide and folate binding sites. PeerJ 2018; 6:e5023. [PMID: 29922516 PMCID: PMC6005164 DOI: 10.7717/peerj.5023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/23/2018] [Indexed: 12/21/2022] Open
Abstract
Thymidylate synthase (TS, E.C. 2.1.1.45) is a crucial enzyme for de novo deoxythymidine monophosphate (dTMP) biosynthesis. The gene for this enzyme is thyA, which encodes the folate-dependent TS that converts deoxyuridine monophosphate group (dUMP) into (dTMP) using the cofactor 5,10-methylenetetrahydrofolate (mTHF) as a carbon donor. We identified the thyA gene in the genome of the Vibrio parahaemolyticus strain FIM-S1708+ that is innocuous to humans but pathogenic to crustaceans. Surprisingly, we found changes in the residues that bind the substrate dUMP and mTHF, previously postulated as invariant among all TSs known (Finer-Moore, Santi & Stroud, 2003). Interestingly, those amino acid changes were also found in a clade of microorganisms that contains Vibrionales, Alteromonadales, Aeromonadales, and Pasteurellales (VAAP) from the Gammaproteobacteria class. In this work, we studied the biochemical properties of recombinant TS from V. parahemolyticus FIM-S1708+ (VpTS) to address the natural changes in the TS amino acid sequence of the VAAP clade. Interestingly, the Km for dUMP was 27.3 ± 4.3 µM, about one-fold larger compared to other TSs. The Km for mTHF was 96.3 ± 18 µM, about three- to five-fold larger compared to other species, suggesting also loss of affinity. Thus, the catalytic efficiency was between one or two orders of magnitude smaller for both substrates. We used trimethoprim, a common antibiotic that targets both TS and DHFR for inhibition studies. The IC50 values obtained were high compared to other results in the literature. Nonetheless, this molecule could be a lead for the design antibiotics towards pathogens from the VAAP clade. Overall, the experimental results also suggest that in the VAAP clade the nucleotide salvage pathway is important and should be investigated, since the de novo dTMP synthesis appears to be compromised by a less efficient thymidylate synthase.
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Affiliation(s)
- Alonso A Lopez-Zavala
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico.,Departamento de Ciencias Quimico Biologicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Eduardo Guevara-Hernandez
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Luz H Vazquez-Lujan
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Arturo Sanchez-Paz
- Laboratorio de Referencia, Análisis y Diagnóstico en Sanidad Acuícola, Centro de Investigaciones Biologicas del Noroeste, Hermosillo, Sonora, Mexico
| | - Karina D Garcia-Orozco
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Carmen A Contreras-Vergara
- Laboratorio de Genetica de Plantas, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
| | - Gamaliel Lopez-Leal
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Aldo A Arvizu-Flores
- Departamento de Ciencias Quimico Biologicas, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rogerio R Sotelo-Mundo
- Biomolecular Structure Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico
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33
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Biswas A, Shukla A, Chaudhary SK, Santhosh R, Jeyakanthan J, Sekar K. Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate. FEBS J 2017. [PMID: 28627020 DOI: 10.1111/febs.14140] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Thymidylate kinase (TMK) is a key enzyme which plays an important role in DNA synthesis. It belongs to the family of nucleoside monophosphate kinases, several of which undergo structure-encoded conformational changes to perform their function. However, the absence of three-dimensional structures for all the different reaction intermediates of a single TMK homolog hinders a clear understanding of its functional mechanism. We herein report the different conformational states along the reaction coordinate of a hyperthermophilic TMK from Aquifex aeolicus, determined via X-ray diffraction and further validated through normal-mode studies. The analyses implicate an arginine residue in the Lid region in catalysis, which was confirmed through site-directed mutagenesis and subsequent enzyme assays on the wild-type protein and mutants. Furthermore, the enzyme was found to exhibit broad specificity toward phosphate group acceptor nucleotides. Our comprehensive analyses of the conformational landscape of TMK, together with associated biochemical experiments, provide insights into the mechanistic details of TMK-driven catalysis, for example, the order of substrate binding and the reaction mechanism for phosphate transfer. Such a study has utility in the design of potent inhibitors for these enzymes. DATABASE Structural data are available in the PDB under the accession numbers 2PBR, 4S2E, 5H5B, 5XAI, 4S35, 5XB2, 5H56, 5XB3, 5H5K, 5XB5, and 5XBH.
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Affiliation(s)
- Ansuman Biswas
- Department of Physics, Indian Institute of Science, Bangalore, India
| | - Arpit Shukla
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | | | | | | | - Kanagaraj Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
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34
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Song L, Risseeuw MDP, Froeyen M, Karalic I, Goeman J, Cappoen D, Van der Eycken J, Cos P, Munier-Lehmann H, Van Calenbergh S. Elaboration of a proprietary thymidylate kinase inhibitor motif towards anti-tuberculosis agents. Bioorg Med Chem 2016; 24:5172-5182. [PMID: 27614917 DOI: 10.1016/j.bmc.2016.08.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 08/20/2016] [Accepted: 08/22/2016] [Indexed: 02/02/2023]
Abstract
We report the design and synthesis of a series of non-nucleoside MtbTMPK inhibitors (1-14) based on the gram-positive bacterial TMPK inhibitor hit compound 1. A practical synthesis was developed to access these analogues. Several compounds show promising MtbTMPK inhibitory potency and allow the establishment of a structure-activity relationship, which is helpful for further optimization.
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Affiliation(s)
- Lijun Song
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteemweg 460, B-9000 Ghent, Belgium
| | - Martijn D P Risseeuw
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteemweg 460, B-9000 Ghent, Belgium
| | - Matheus Froeyen
- Medicinal Chemistry (Rega Institute), Department of Pharmaceutical and Pharmacological Sciences, KU LEUVEN, Minderbroedersstraat 10 blok x-box 1030, 3000 Leuven, Belgium
| | - Izet Karalic
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteemweg 460, B-9000 Ghent, Belgium
| | - Jan Goeman
- Laboratory for Organic and Bioorganic Synthesis, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4, B-9000 Ghent, Belgium
| | - Davie Cappoen
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Department of Pharmaceutical Sciences, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, B-2610 Antwerpen,. Belgium
| | - Johan Van der Eycken
- Laboratory for Organic and Bioorganic Synthesis, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4, B-9000 Ghent, Belgium
| | - Paul Cos
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), Department of Pharmaceutical Sciences, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, B-2610 Antwerpen,. Belgium
| | - Hélène Munier-Lehmann
- Institut Pasteur, Unit of Chemistry and Biocatalysis, Department of Structural Biology and Chemistry, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France; CNRS UMR3523, Paris, France
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteemweg 460, B-9000 Ghent, Belgium.
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Chen YH, Hsu HY, Yeh MT, Chen CC, Huang CY, Chung YH, Chang ZF, Kuo WC, Chan NL, Weng JH, Chung BC, Chen YJ, Jian CB, Shen CC, Tai HC, Sheu SY, Fang JM. Chemical Inhibition of Human Thymidylate Kinase and Structural Insights into the Phosphate Binding Loop and Ligand-Induced Degradation. J Med Chem 2016; 59:9906-9918. [DOI: 10.1021/acs.jmedchem.6b01280] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yi-Hsuan Chen
- Department
of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Hua-Yi Hsu
- Department
of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Ming-Tyng Yeh
- Department
of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Chen-Cheng Chen
- Graduate
Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Chang-Yu Huang
- Graduate
Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Ying-Hsuan Chung
- Graduate
Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Zee-Fen Chang
- Graduate
Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Wei-Chen Kuo
- Institute
of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Nei-Li Chan
- Institute
of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Jui-Hsia Weng
- Institute
of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Bon-chu Chung
- Institute
of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ju Chen
- Department
of Chemistry, National Taiwan University, Taipei 106, Taiwan
- Institute
of Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Cheng-Bang Jian
- Department
of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Ching-Chieh Shen
- Department
of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Hwan-Ching Tai
- Department
of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Sheh-Yi Sheu
- Department
of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
- Institute
of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan
| | - Jim-Min Fang
- Department
of Chemistry, National Taiwan University, Taipei 106, Taiwan
- The
Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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36
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Abstract
The first synthesis of carbasugars, compounds in which the ring oxygen of a monosaccharide had been replaced by a methylene moiety, was described in 1966 by Professor G. E. McCasland’s group. Seven years later, the first true natural carbasugar (5a-carba-R-D-galactopyranose) was isolated from a fermentation broth of Streptomyces sp. MA-4145. In the following decades, the chemistry and biology of carbasugars have been extensively studied. Most of these compounds show interesting biological properties, especially enzymatic inhibitory activities, and, in consequence, an important number of analogues have also been prepared in the search for improved biological activities. The aim of this review is to give coverage on the progress made in two important aspects of these compounds: the elucidation of their biosynthesis and the consideration of their biological properties, including the extensively studied carbapyranoses as well as the much less studied carbafuranoses.
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Nyíri K, Vértessy BG. Perturbation of genome integrity to fight pathogenic microorganisms. Biochim Biophys Acta Gen Subj 2016; 1861:3593-3612. [PMID: 27217086 DOI: 10.1016/j.bbagen.2016.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Resistance against antibiotics is unfortunately still a major biomedical challenge for a wide range of pathogens responsible for potentially fatal diseases. SCOPE OF REVIEW In this study, we aim at providing a critical assessment of the recent advances in design and use of drugs targeting genome integrity by perturbation of thymidylate biosynthesis. MAJOR CONCLUSION We find that research efforts from several independent laboratories resulted in chemically highly distinct classes of inhibitors of key enzymes within the routes of thymidylate biosynthesis. The present article covers numerous studies describing perturbation of this metabolic pathway in some of the most challenging pathogens like Mycobacterium tuberculosis, Plasmodium falciparum, and Staphylococcus aureus. GENERAL SIGNIFICANCE Our comparative analysis allows a thorough summary of the current approaches to target thymidylate biosynthesis enzymes and also include an outlook suggesting novel ways of inhibitory strategies. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Kinga Nyíri
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
| | - Beáta G Vértessy
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
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38
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Untargeted Metabolomics To Ascertain Antibiotic Modes of Action. Antimicrob Agents Chemother 2016; 60:2281-91. [PMID: 26833150 PMCID: PMC4808186 DOI: 10.1128/aac.02109-15] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/31/2016] [Indexed: 01/23/2023] Open
Abstract
Deciphering the mode of action (MOA) of new antibiotics discovered through phenotypic screening is of increasing importance. Metabolomics offers a potentially rapid and cost-effective means of identifying modes of action of drugs whose effects are mediated through changes in metabolism. Metabolomics techniques also collect data on off-target effects and drug modifications. Here, we present data from an untargeted liquid chromatography-mass spectrometry approach to identify the modes of action of eight compounds: 1-[3-fluoro-4-(5-methyl-2,4-dioxo-pyrimidin-1-yl)phenyl]-3-[2-(trifluoromethyl)phenyl]urea (AZ1), 2-(cyclobutylmethoxy)-5'-deoxyadenosine, triclosan, fosmidomycin, CHIR-090, carbonyl cyanidem-chlorophenylhydrazone (CCCP), 5-chloro-2-(methylsulfonyl)-N-(1,3-thiazol-2-yl)-4-pyrimidinecarboxamide (AZ7), and ceftazidime. Data analysts were blind to the compound identities but managed to identify the target as thymidylate kinase for AZ1, isoprenoid biosynthesis for fosmidomycin, acyl-transferase for CHIR-090, and DNA metabolism for 2-(cyclobutylmethoxy)-5'-deoxyadenosine. Changes to cell wall metabolites were seen in ceftazidime treatments, although other changes, presumably relating to off-target effects, dominated spectral outputs in the untargeted approach. Drugs which do not work through metabolic pathways, such as the proton carrier CCCP, have no discernible impact on the metabolome. The untargeted metabolomics approach also revealed modifications to two compounds, namely, fosmidomycin and AZ7. An untreated control was also analyzed, and changes to the metabolome were seen over 4 h, highlighting the necessity for careful controls in these types of studies. Metabolomics is a useful tool in the analysis of drug modes of action and can complement other technologies already in use.
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Abstract
Purine and pyrimidine nucleoside and nucleotide analogs have been extensively studied as anticancer and antiviral agents. In addition to this, they have recently shown great potential against Mycobacterium Tuberculosis, the causative agent of TB. TB ranks as the tenth most common cause of death in the world. The current treatment for TB infection is limited by side effects and cost of the drugs and most importantly by the development of resistance to the therapy. Therefore the development of novel drugs, capable of overcoming the drawbacks of the existing treatments, has become the focus of many research programs. In parallel to that, a tremendous effort has been made to elucidate the unique metabolism of this pathogen with the aim to identify new possible targets. This review presents the state of the art in nucleoside and nucleotide analogs in the treatment of TB. In particular, we report on the inhibitory activity of this class of compounds, both in enzymatic and whole-cell assays, providing a brief insight to which reported target these novel compounds are hitting.
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40
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Kazakiewicz D, Karr JR, Langner KM, Plewczynski D. A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium. Comput Biol Chem 2015; 59 Pt B:91-7. [DOI: 10.1016/j.compbiolchem.2015.07.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/05/2015] [Accepted: 07/24/2015] [Indexed: 12/13/2022]
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41
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Ardisson-Araújo DMP, de Melo FL, Andrade MDS, Sihler W, Báo SN, Ribeiro BM, de Souza ML. Genome sequence of Erinnyis ello granulovirus (ErelGV), a natural cassava hornworm pesticide and the first sequenced sphingid-infecting betabaculovirus. BMC Genomics 2014; 15:856. [PMID: 25280947 PMCID: PMC4192325 DOI: 10.1186/1471-2164-15-856] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 09/25/2014] [Indexed: 12/03/2022] Open
Abstract
Background Cassava (Manihot esculenta) is the basic source for dietary energy of 500 million people in the world. In Brazil, Erinnyis ello ello (Lepidoptera: Sphingidae) is a major pest of cassava crops and a bottleneck for its production. In the 1980s, a naturally occurring baculovirus was isolated from E. ello larva and successfully applied as a bio-pesticide in the field. Here, we described the structure, the complete genome sequence, and the phylogenetic relationships of the first sphingid-infecting betabaculovirus. Results The baculovirus isolated from the cassava hornworm cadavers is a betabaculovirus designated Erinnyis ello granulovirus (ErelGV). The 102,759 bp long genome has a G + C content of 38.7%. We found 130 putative ORFs coding for polypeptides of at least 50 amino acid residues. Only eight genes were found to be unique. ErelGV is closely related to ChocGV and PiraGV isolates. We did not find typical homologous regions and cathepsin and chitinase homologous genes are lacked. The presence of he65 and p43 homologous genes suggests horizontal gene transfer from Alphabaculovirus. Moreover, we found a nucleotide metabolism-related gene and two genes that could be acquired probably from Densovirus. Conclusions The ErelGV represents a new virus species from the genus Betabaculovirus and is the closest relative of ChocGV. It contains a dUTPase-like, a he65-like, p43-like genes, which are also found in several other alpha- and betabaculovirus genomes, and two Densovirus-related genes. Importantly, recombination events between insect viruses from unrelated families and genera might drive baculovirus genomic evolution. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-856) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Bergmann Morais Ribeiro
- Cell Biology Department, Laboratory of Baculovirus, University of Brasília, 70910-900 Brasília, DF, Brazil.
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