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Gomes AFT, de Medeiros WF, Medeiros I, Piuvezam G, da Silva-Maia JK, Bezerra IWL, Morais AHDA. In Silico Screening of Therapeutic Targets as a Tool to Optimize the Development of Drugs and Nutraceuticals in the Treatment of Diabetes mellitus: A Systematic Review. Int J Mol Sci 2024; 25:9213. [PMID: 39273161 PMCID: PMC11394750 DOI: 10.3390/ijms25179213] [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: 07/18/2024] [Revised: 08/16/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
The Target-Based Virtual Screening approach is widely employed in drug development, with docking or molecular dynamics techniques commonly utilized for this purpose. This systematic review (SR) aimed to identify in silico therapeutic targets for treating Diabetes mellitus (DM) and answer the question: What therapeutic targets have been used in in silico analyses for the treatment of DM? The SR was developed following the guidelines of the Preferred Reporting Items Checklist for Systematic Review and Meta-Analysis, in accordance with the protocol registered in PROSPERO (CRD42022353808). Studies that met the PECo strategy (Problem, Exposure, Context) were included using the following databases: Medline (PubMed), Web of Science, Scopus, Embase, ScienceDirect, and Virtual Health Library. A total of 20 articles were included, which not only identified therapeutic targets in silico but also conducted in vivo analyses to validate the obtained results. The therapeutic targets most frequently indicated in in silico studies were GLUT4, DPP-IV, and PPARγ. In conclusion, a diversity of targets for the treatment of DM was verified through both in silico and in vivo reassessment. This contributes to the discovery of potential new allies for the treatment of DM.
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Affiliation(s)
- Ana Francisca T Gomes
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
| | - Wendjilla F de Medeiros
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
| | - Isaiane Medeiros
- Biochemistry and Molecular Biology Postgraduate Program, Biosciences Center, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
| | - Grasiela Piuvezam
- Public Health Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
| | - Juliana Kelly da Silva-Maia
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
- Department of Nutrition, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
| | - Ingrid Wilza L Bezerra
- Department of Nutrition, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
| | - Ana Heloneida de A Morais
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
- Biochemistry and Molecular Biology Postgraduate Program, Biosciences Center, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
- Department of Nutrition, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
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Khan MF, Ali A, Rehman HM, Noor Khan S, Hammad HM, Waseem M, Wu Y, Clark TG, Jabbar A. Exploring optimal drug targets through subtractive proteomics analysis and pangenomic insights for tailored drug design in tuberculosis. Sci Rep 2024; 14:10904. [PMID: 38740859 DOI: 10.1038/s41598-024-61752-6] [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: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, ranks among the top causes of global human mortality, as reported by the World Health Organization's 2022 TB report. The prevalence of M. tuberculosis strains that are multiple and extensive-drug resistant represents a significant barrier to TB eradication. Fortunately, having many completely sequenced M. tuberculosis genomes available has made it possible to investigate the species pangenome, conduct a pan-phylogenetic investigation, and find potential new drug targets. The 442 complete genome dataset was used to estimate the pangenome of M. tuberculosis. This study involved phylogenomic classification and in-depth analyses. Sequential filters were applied to the conserved core genome containing 2754 proteins. These filters assessed non-human homology, virulence, essentiality, physiochemical properties, and pathway analysis. Through these intensive filtering approaches, promising broad-spectrum therapeutic targets were identified. These targets were docked with FDA-approved compounds readily available on the ZINC database. Selected highly ranked ligands with inhibitory potential include dihydroergotamine and abiraterone acetate. The effectiveness of the ligands has been supported by molecular dynamics simulation of the ligand-protein complexes, instilling optimism that the identified lead compounds may serve as a robust basis for the development of safe and efficient drugs for TB treatment, subject to further lead optimization and subsequent experimental validation.
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Affiliation(s)
- Muhammad Fayaz Khan
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, KP, Pakistan
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Sadiq Noor Khan
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, KP, Pakistan
| | - Hafiz Muhammad Hammad
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Punjab, Pakistan
| | - Maaz Waseem
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Yurong Wu
- Department of Chemistry, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Taane G Clark
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK.
| | - Abdul Jabbar
- Department of Medical Laboratory Technology, The University of Haripur, Haripur, KP, Pakistan.
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Sarker P, Mitro A, Hoque H, Hasan MN, Nurnabi Azad Jewel GM. Identification of potential novel therapeutic drug target against Elizabethkingia anophelis by integrative pan and subtractive genomic analysis: An in silico approach. Comput Biol Med 2023; 165:107436. [PMID: 37690289 DOI: 10.1016/j.compbiomed.2023.107436] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 07/08/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
Elizabethkingia anophelis is a human pathogen responsible for severe nosocomial infections in neonates and immunocompromised patients. The significantly higher mortality rate from E. anophelis infections and the lack of available regimens highlight the critical need to explore novel drug targets. The current study investigated effective novel drug targets by employing a comprehensive in silico subtractive genomic approach integrated with pangenomic analysis of E. anophelis strains. A total of 2809 core genomic proteins were found by pangenomic analysis of non-paralogous proteins. Subsequently, 156 pathogen-specific, 442 choke point, 202 virulence factor, 53 antibiotic resistant and 119 host-pathogen interacting proteins were identified in E. anophelis. By subtractive genomic approach, at first 791 proteins were found to be indispensable for the survival of E. anophelis. 558 and 315 proteins were detected as non-homologous to human and gut microflora respectively. Following that 245 cytoplasmic, 245 novel, and 23 broad-spectrum targets were selected and finally four proteins were considered as potential therapeutic targets of E. anophelis based on highest degree score in PPI network. Among those, three proteins were subjected to molecular docking and subsequent MD simulation as one protein did not contain a plausible binding pocket with sufficient surface area and volume. All the complexes were found to be stable and compact in 100 ns molecular dynamics simulation studies as measured by RMSD, RMSF, and Rg. These three short-listed targets identified in this study may lead to the development of novel antimicrobials capable of curing infections and pave the way to prevent and control the disease progression caused by the deadly agent E. anophelis.
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Affiliation(s)
- Parth Sarker
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh
| | - Arnob Mitro
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh
| | - Hammadul Hoque
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh
| | - Md Nazmul Hasan
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh
| | - G M Nurnabi Azad Jewel
- Dept. of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, University Ave, Sylhet-3114, Bangladesh; Computational Biology and Bioinformatics Lab, Dept. of GEB, SUST, Sylhet-3114, Bangladesh.
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Qureshi KA, Azam F, Fatmi MQ, Imtiaz M, Prajapati DK, Rai PK, Jaremko M, Emwas AH, Elhassan GO. In vitro and in silico evaluations of actinomycin X 2and actinomycin D as potent anti-tuberculosis agents. PeerJ 2023; 11:e14502. [PMID: 36935926 PMCID: PMC10022501 DOI: 10.7717/peerj.14502] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 11/10/2022] [Indexed: 03/11/2023] Open
Abstract
Background Multidrug-resistant tuberculosis (MDR-TB) is one of the world's most devastating contagious diseases and is caused by the MDR-Mycobacterium tuberculosis (MDR-Mtb) bacteria. It is therefore essential to identify novel anti-TB drug candidates and target proteins to treat MDR-TB. Here, in vitro and in silico studies were used to investigate the anti-TB potential of two newly sourced actinomycins, actinomycin-X2 (act-X2) and actinomycin-D (act-D), from the Streptomyces smyrnaeus strain UKAQ_23 (isolated from the Jubail industrial city of Saudi Arabia). Methods The anti-TB activity of the isolated actinomycins was assessed in vitro using the Mtb H37Ra, Mycobacterium bovis (BCG), and Mtb H37Rv bacterial strains, using the Microplate Alamar Blue Assay (MABA) method. In silico molecular docking studies were conducted using sixteen anti-TB drug target proteins using the AutoDock Vina 1.1.2 tool. The molecular dynamics (MD) simulations for both actinomycins were then performed with the most suitable target proteins, using the GROningen MAchine For Chemical Simulations (GROMACS) simulation software (GROMACS 2020.4), with the Chemistry at HARvard Macromolecular Mechanics 36m (CHARMM36m) forcefield for proteins and the CHARMM General Force Field (CGenFF) for ligands. Results In vitro results for the Mtb H37Ra, BCG, and Mtb H37Rv strains showed that act-X2 had minimum inhibitory concentration (MIC) values of 1.56 ± 0.0, 1.56 ± 0.0, and 2.64 ± 0.07 µg/mL and act-D had MIC values of 1.56 ± 0.0, 1.56 ± 0.0, and 1.80 ± 0.24 µg/mL respectively. The in silico molecular docking results showed that protein kinase PknB was the preferred target for both actinomycins, while KasA and pantothenate synthetase were the least preferred targets for act-X2and act-D respectively. The molecular dynamics (MD) results demonstrated that act-X2 and act-D remained stable inside the binding region of PknB throughout the simulation period. The MM/GBSA (Molecular Mechanics/Generalized Born Surface Area) binding energy calculations showed that act-X2 was more potent than act-D. Conclusion In conclusion, our results suggest that both actinomycins X2 and D are highly potent anti-TB drug candidates. We show that act-X2is better able to antagonistically interact with the protein kinase PknB target than act-D, and thus has more potential as a new anti-TB drug candidate.
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Affiliation(s)
- Kamal Ahmad Qureshi
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Al-Qassim, Saudi Arabia
| | - Faizul Azam
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Unaizah, Al-Qassim, Saudi Arabia
| | | | - Mahrukh Imtiaz
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Dinesh Kumar Prajapati
- Department of Biotechnology, Faculty of Biosciences, Invertis University, Bareilly, Uttar Pradesh, India
| | - Pankaj Kumar Rai
- Department of Biotechnology, Faculty of Biosciences, Invertis University, Bareilly, Uttar Pradesh, India
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Saudi Arabia
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gamal Osman Elhassan
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Al-Qassim, Saudi Arabia
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Gomes AFT, de Medeiros WF, de Oliveira GS, Medeiros I, Maia JKDS, Bezerra IWL, Piuvezam G, Morais AHDA. In silico structure-based designers of therapeutic targets for diabetes mellitus or obesity: A protocol for systematic review. PLoS One 2022; 17:e0279039. [PMID: 36508447 PMCID: PMC9744281 DOI: 10.1371/journal.pone.0279039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Obesity is a significant risk factor for several chronic non-communicable diseases, being closely related to Diabetes Mellitus. Computer modeling techniques favor the understanding of interaction mechanisms between specific targets and substances of interest, optimizing drug development. In this article, the protocol of two protocols of systematic reviews are described for identifying therapeutic targets and models for treating obesity or diabetes mellitus investigated in silico. The protocol is by the guidelines from the Preferred Reporting Items for Systematic Reviews and Meta-Analyzes Protocols (PRISMA-P) and was published in the International Prospective Register of Systematic Reviews database (PROSPERO: CRD42022353808). Search strategies will be developed based on the combination of descriptors and executed in the following databases: PubMed; ScienceDirect; Scopus; Web of Science; Virtual Health Library; EMBASE. Only original in silico studies with molecular dynamics, molecular docking, or both will be inserted. Two trained researchers will independently select the articles, extract the data, and assess the risk of bias. The quality will be assessed through an adapted version of the Strengthening the Reporting of Empirical Simulation Studies (STRESS) and the risk of bias using a checklist obtained from separate literature sources. The implementation of this protocol will result in the elaboration of two systematic reviews identifying the therapeutic targets for treating obesity (review 1) or diabetes mellitus (review 2) used in computer simulation studies and their models. The systematization of knowledge about these treatment targets and their in silico structures is fundamental, primarily because computer simulation contributes to more accurate planning of future either in vitro or in vivo studies. Therefore, the reviews developed from this protocol will guide decision-making regarding the choice of targets/models in future research focused on therapeutics of obesity or Diabetes Mellitus contributing to mitigate of factors such as costs, time, and necessity of in vitro and/or in vivo assays.
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Affiliation(s)
- Ana Francisca Teixeira Gomes
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | | | - Gerciane Silva de Oliveira
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Isaiane Medeiros
- Biochemistry and Molecular Biology Postgraduate Program, Biosciences Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Juliana Kelly da Silva Maia
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Department of Nutrition, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Ingrid Wilza Leal Bezerra
- Department of Nutrition, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Grasiela Piuvezam
- Public Health Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Public Health, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Ana Heloneida de Araújo Morais
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Biochemistry and Molecular Biology Postgraduate Program, Biosciences Center, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Nutrition, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- * E-mail:
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Discovery of novel DprE1 inhibitors via computational bioactivity fingerprints and structure-based virtual screening. Acta Pharmacol Sin 2022; 43:1605-1615. [PMID: 34667293 PMCID: PMC9160271 DOI: 10.1038/s41401-021-00779-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/16/2021] [Indexed: 02/07/2023] Open
Abstract
Decaprenylphosphoryl-β-D-ribose oxidase (DprE1) plays important roles in the biosynthesis of mycobacterium cell wall. DprE1 inhibitors have shown great potentials in the development of new regimens for tuberculosis (TB) treatment. In this study, an integrated molecular modeling strategy, which combined computational bioactivity fingerprints and structure-based virtual screening, was employed to identify potential DprE1 inhibitors. Two lead compounds (B2 and H3) that could inhibit DprE1 and thus kill Mycobacterium smegmatis in vitro were identified. Moreover, compound H3 showed potent inhibitory activity against Mycobacterium tuberculosis in vitro (MICMtb = 1.25 μM) and low cytotoxicity against mouse embryo fibroblast NIH-3T3 cells. Our research provided an effective strategy to discover novel anti-TB lead compounds.
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Calixto SD, Simão TLBV, de Almeida FM, Antunes SS, Romeiro NC, de Souza Borges W, das Chagas FO, Seldin L, de Carvalho ECQ, Andrioli WJ, Guimarães DO, Lasunskaia E, Muzitano MF. (R)-(+)-Lasiodiplodin isolated from the endophytic fungus Sordaria tamaensis exhibits potent antimycobacterial and anti-inflammatory activities in vitro and in vivo: a dual approach for the treatment of severe pulmonary tuberculosis. J Pharm Pharmacol 2021; 74:446-457. [PMID: 34850064 DOI: 10.1093/jpp/rgab165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVES This study aimed to evaluate endophytic fungi isolated from Tocoyena bullata and Humiria balsamifera plant species for their antimycobacterial and anti-inflammatory activities, focusing on severe pulmonary tuberculosis cases which are often associated with exacerbated inflammation. METHODS Mycobacterium suspensions were incubated with the samples for 5 days. RAW 264.7 macrophages stimulated with LPS were also incubated with them for 24 h to assess the inhibition of inflammatory mediator production and cytotoxicity. C57BL/6 mice were infected with Mtb M299 and treated for 15 days with lasiodiplodin (Lasio). KEY FINDINGS Endophytic fungus Sordaria tamaensis, obtained from T. bullata, was the most promising. Its ethanolic extract impaired mycobacterial growth with MIC50 (µg/ml): 1.5 ± 0.6 (BCG), 66.8 ± 0.1 (H37Rv) and 80.0 ± 0.1 (M299). (R)-(+)-Lasio showed MIC50 92.2 ± 1.8 µg/ml (M299). In addition, Lasio was able to inhibit NO, IL-1β and TNF-α production and was not cytotoxic for macrophages. M. tuberculosis-infected C57BL/6 animals treated by Lasio reduced the number of acid-fast bacilli, lung pathology, leucocyte influx and proinflammatory cytokine production in the lungs. The class IIa fructose 1,6-bisphosphate aldolase was the predicted hypothetical target of Lasio. CONCLUSIONS (R)-(+)-Lasio stood out as a promising anti-TB compound, exhibiting anti-inflammatory and antimycobacterial effects, as well as low cytotoxicity.
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Affiliation(s)
- Sanderson Dias Calixto
- Laboratório de Biologia do Reconhecer, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil.,Laboratório de Produtos Bioativos, Curso de Farmácia, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
| | - Thatiana Lopes Biá Ventura Simão
- Laboratório de Produtos Bioativos, Curso de Farmácia, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
| | - Fabrício Moreira de Almeida
- Laboratório de Biologia do Reconhecer, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Stella Schuenck Antunes
- Laboratório Integrado de Computação Científica, Programa de Pós Graduação em Produtos Bioativos e Biociências, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
| | - Nelilma Correia Romeiro
- Laboratório Integrado de Computação Científica, Programa de Pós Graduação em Produtos Bioativos e Biociências, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
| | - Warley de Souza Borges
- Departamento de Química, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Fernanda Oliveira das Chagas
- Instituto de Pesquisa de Produtos Naturais Walter Mors, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucy Seldin
- Laboratório de Genética Microbiana CCS, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Willian Jonis Andrioli
- Laboratório de Produtos Bioativos, Curso de Farmácia, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
| | - Denise Oliveira Guimarães
- Laboratório de Produtos Bioativos, Curso de Farmácia, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
| | - Elena Lasunskaia
- Laboratório de Biologia do Reconhecer, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Michelle Frazão Muzitano
- Laboratório de Produtos Bioativos, Curso de Farmácia, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
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Pangenome Analysis of Mycobacterium tuberculosis Reveals Core-Drug Targets and Screening of Promising Lead Compounds for Drug Discovery. Antibiotics (Basel) 2020; 9:antibiotics9110819. [PMID: 33213029 PMCID: PMC7698547 DOI: 10.3390/antibiotics9110819] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 12/03/2022] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis (M. tuberculosis), is one of the leading causes of human deaths globally according to the WHO TB 2019 report. The continuous rise in multi- and extensive-drug resistance in M. tuberculosis broadens the challenges to control tuberculosis. The availability of a large number of completely sequenced genomes of M. tuberculosis has provided an opportunity to explore the pangenome of the species along with the pan-phylogeny and to identify potential novel drug targets leading to drug discovery. We attempt to calculate the pangenome of M. tuberculosis that comprises a total of 150 complete genomes and performed the phylo-genomic classification and analysis. Further, the conserved core genome (1251 proteins) is subjected to various sequential filters (non-human homology, essentiality, virulence, physicochemical parameters, and pathway analysis) resulted in identification of eight putative broad-spectrum drug targets. Upon molecular docking analyses of these targets with ligands available at the DrugBank database shortlisted a total of five promising ligands with projected inhibitory potential; namely, 2′deoxy-thymidine-5′-diphospho-alpha-d-glucose, uridine diphosphate glucose, 2′-deoxy-thymidine-beta-l-rhamnose, thymidine-5′-triphosphate, and citicoline. We are confident that with further lead optimization and experimental validation, these lead compounds may provide a sound basis to develop safe and effective drugs against tuberculosis disease in humans.
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Favero LM, Chideroli RT, Ferrari NA, Azevedo VADC, Tiwari S, Lopera-Barrero NM, Pereira UDP. In silico Prediction of New Drug Candidates Against the Multidrug-Resistant and Potentially Zoonotic Fish Pathogen Serotype III Streptococcus agalactiae. Front Genet 2020; 11:1024. [PMID: 33005185 PMCID: PMC7484375 DOI: 10.3389/fgene.2020.01024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/11/2020] [Indexed: 12/02/2022] Open
Abstract
Streptococcus agalactiae is an invasive multi-host pathogen that causes invasive diseases mainly in newborns, elderly, and individuals with underlying health complications. In fish, S. agalactiae causes streptococcosis, which is characterized by septicemia and neurological signs, and leads to great economic losses to the fish farming industry worldwide. These bacteria can be classified into different serotypes based on capsular antigens, and into different sequence types (ST) based on multilocus sequence typing (MLST). In 2015, serotype III ST283 was identified to be associated with a foodborne invasive disease in non-pregnant immunocompetent humans in Singapore, and the infection was related to raw fish consumption. In addition, a serotype III strain isolated from tilapia in Brazil has been reported to be resistant to five antibiotic classes. This specific serotype can serve as a reservoir of resistance genes and pose a serious threat to public health. Thus, new approaches for the control and treatment of S. agalactiae infections are needed. In the present study, 24 S. agalactiae serotype III complete genomes, isolated from human and fish hosts, were compared. The core genome was identified, and, using bioinformatics tools and subtractive criteria, five proteins were identified as potential drug targets. Furthermore, 5,008 drug-like natural compounds were virtually screened against the identified targets. The ligands with the best binding properties are suggested for further in vitro and in vivo analysis.
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Affiliation(s)
- Leonardo Mantovani Favero
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Roberta Torres Chideroli
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Natália Amoroso Ferrari
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Vasco Ariston De Carvalho Azevedo
- Institute of Biological Sciences, Department of Genetic, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Sandeep Tiwari
- Institute of Biological Sciences, Department of Genetic, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Ulisses de Pádua Pereira
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
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Rahul Reddy MB, Krishnasamy SK, Kathiravan MK. Identification of novel scaffold using ligand and structure based approach targeting shikimate kinase. Bioorg Chem 2020; 102:104083. [PMID: 32745735 DOI: 10.1016/j.bioorg.2020.104083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 10/23/2022]
Abstract
Tuberculosis (TB) remains a major global health problem. It causes ill-health among millions of people each year and rank as the second leading cause of death from an infectious disease worldwide, after the human immunodeficiency virus (HIV). Shikimate kinase is one of the major enzymes targeted for TB. Most approaches to overcome TB were based on synthesis and screening of a known compounds to obtain a few representatives with desired potency. In this study, we have applied a virtual screening approach which combines ligand- and structure-based approaches to screen a large library of compounds as a starting point for the identification of new scaffolds for the development of shikimate kinase inhibitors. The combined approach has identified 2 new scaffolds as potential inhibitors of shikimate kinase. To prove the approach, few of the molecules and their derivatives, a total of 17 compounds, were synthesized. The compounds were tested for biological activity and shows moderate activity against shikimate kinase. The shikimate kinase enzyme inhibition study reveals that the compounds showed inhibition (IC50) at concentrations of 50 µg/mL (Compounds 21, 22, 24, 25, 26, 27, 30, 32, 34) and 25 µg/mL (14, 19, 23, 31, 33).
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Affiliation(s)
- M B Rahul Reddy
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu 603203, India
| | | | - M K Kathiravan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu 603203, India; 209, Dr APJ Abdul Kalam Research Lab, SRM College of Pharmacy, SRM IST Kattankulathur, Kancheepuram, Tamil Nadu 603203, India
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