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Nogueira WG, Jaiswal AK, Tiwari S, Ramos RTJ, Ghosh P, Barh D, Azevedo V, Soares SC. Computational identification of putative common genomic drug and vaccine targets in Mycoplasma genitalium. Genomics 2021; 113:2730-2743. [PMID: 34118385 DOI: 10.1016/j.ygeno.2021.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/17/2021] [Accepted: 06/07/2021] [Indexed: 10/21/2022]
Abstract
Mycoplasma genitalium is an obligate intracellular bacterium that is responsible for several sexually transmitted infections, including non-gonococcal urethritis in men and several inflammatory reproductive tract syndromes in women. Here, we applied subtractive genomics and reverse vaccinology approaches for in silico prediction of potential vaccine and drug targets against five strains of M. genitalium. We identified 403 genes shared by all five strains, from which 104 non-host homologous proteins were selected, comprising of 44 exposed/secreted/membrane proteins and 60 cytoplasmic proteins. Based on the essentiality, functionality, and structure-based binding affinity, we finally predicted 19 (14 novel) putative vaccine and 7 (2 novel) candidate drug targets. The docking analysis showed six molecules from the ZINC database as promising drug candidates against the identified targets. Altogether, both vaccine candidates and drug targets identified here may contribute to the future development of therapeutic strategies to control the spread of M. genitalium worldwide.
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Affiliation(s)
- Wylerson G Nogueira
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas,Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Arun Kumar Jaiswal
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas,Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.; Department of Immunology, Microbiology and Parasitology, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas,Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil..
| | - Rommel T J Ramos
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond VA-23284, USA
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, India
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas,Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Siomar C Soares
- Department of Immunology, Microbiology and Parasitology, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil.
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Jamal SB, Hassan SS, Tiwari S, Viana MV, Benevides LDJ, Ullah A, Turjanski AG, Barh D, Ghosh P, Costa DA, Silva A, Röttger R, Baumbach J, Azevedo VAC. An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae. PLoS One 2017; 12:e0186401. [PMID: 29049350 PMCID: PMC5648181 DOI: 10.1371/journal.pone.0186401] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 09/29/2017] [Indexed: 01/03/2023] Open
Abstract
Corynebacterium diphtheriae (Cd) is a Gram-positive human pathogen responsible for diphtheria infection and once regarded for high mortalities worldwide. The fatality gradually decreased with improved living standards and further alleviated when many immunization programs were introduced. However, numerous drug-resistant strains emerged recently that consequently decreased the efficacy of current therapeutics and vaccines, thereby obliging the scientific community to start investigating new therapeutic targets in pathogenic microorganisms. In this study, our contributions include the prediction of modelome of 13 C. diphtheriae strains, using the MHOLline workflow. A set of 463 conserved proteins were identified by combining the results of pangenomics based core-genome and core-modelome analyses. Further, using subtractive proteomics and modelomics approaches for target identification, a set of 23 proteins was selected as essential for the bacteria. Considering human as a host, eight of these proteins (glpX, nusB, rpsH, hisE, smpB, bioB, DIP1084, and DIP0983) were considered as essential and non-host homologs, and have been subjected to virtual screening using four different compound libraries (extracted from the ZINC database, plant-derived natural compounds and Di-terpenoid Iso-steviol derivatives). The proposed ligand molecules showed favorable interactions, lowered energy values and high complementarity with the predicted targets. Our proposed approach expedites the selection of C. diphtheriae putative proteins for broad-spectrum development of novel drugs and vaccines, owing to the fact that some of these targets have already been identified and validated in other organisms.
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Affiliation(s)
- Syed Babar Jamal
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Syed Shah Hassan
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Chemistry, Islamia College University Peshawar, KPK, Pakistan
| | - Sandeep Tiwari
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marcus V. Viana
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Leandro de Jesus Benevides
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Asad Ullah
- Department of Chemistry, Islamia College University Peshawar, KPK, Pakistan
| | - Adrián G. Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, Buenos Aires, Argentina
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Daniela Arruda Costa
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Artur Silva
- Institute of Biologic Sciences, Federal University of Para, Belém, PA, Brazil
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Vasco A. C. Azevedo
- PG program in Bioinformatics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of General Biology (LGCM), Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- * E-mail:
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An In Silico Identification of Common Putative Vaccine Candidates against Treponema pallidum: A Reverse Vaccinology and Subtractive Genomics Based Approach. Int J Mol Sci 2017; 18:ijms18020402. [PMID: 28216574 PMCID: PMC5343936 DOI: 10.3390/ijms18020402] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/22/2017] [Accepted: 01/27/2017] [Indexed: 01/28/2023] Open
Abstract
Sexually transmitted infections (STIs) are caused by a wide variety of bacteria, viruses, and parasites that are transmitted from one person to another primarily by vaginal, anal, or oral sexual contact. Syphilis is a serious disease caused by a sexually transmitted infection. Syphilis is caused by the bacterium Treponema pallidum subspecies pallidum. Treponema pallidum (T. pallidum) is a motile, gram-negative spirochete, which can be transmitted both sexually and from mother to child, and can invade virtually any organ or structure in the human body. The current worldwide prevalence of syphilis emphasizes the need for continued preventive measures and strategies. Unfortunately, effective measures are limited. In this study, we focus on the identification of vaccine targets and putative drugs against syphilis disease using reverse vaccinology and subtractive genomics. We compared 13 strains of T. pallidum using T. pallidum Nichols as the reference genome. Using an in silicoapproach, four pathogenic islands were detected in the genome of T. pallidum Nichols. We identified 15 putative antigenic proteins and sixdrug targets through reverse vaccinology and subtractive genomics, respectively, which can be used as candidate therapeutic targets in the future.
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Hassan SS, Tiwari S, Guimarães LC, Jamal SB, Folador E, Sharma NB, de Castro Soares S, Almeida S, Ali A, Islam A, Póvoa FD, de Abreu VAC, Jain N, Bhattacharya A, Juneja L, Miyoshi A, Silva A, Barh D, Turjanski AG, Azevedo V, Ferreira RS. Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis. BMC Genomics 2014; 15 Suppl 7:S3. [PMID: 25573232 PMCID: PMC4243142 DOI: 10.1186/1471-2164-15-s7-s3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Corynebacterium pseudotuberculosis (Cp) is a pathogenic bacterium that causes caseous lymphadenitis (CLA), ulcerative lymphangitis, mastitis, and edematous to a broad spectrum of hosts, including ruminants, thereby threatening economic and dairy industries worldwide. Currently there is no effective drug or vaccine available against Cp. To identify new targets, we adopted a novel integrative strategy, which began with the prediction of the modelome (tridimensional protein structures for the proteome of an organism, generated through comparative modeling) for 15 previously sequenced C. pseudotuberculosis strains. This pan-modelomics approach identified a set of 331 conserved proteins having 95-100% intra-species sequence similarity. Next, we combined subtractive proteomics and modelomics to reveal a set of 10 Cp proteins, which may be essential for the bacteria. Of these, 4 proteins (tcsR, mtrA, nrdI, and ispH) were essential and non-host homologs (considering man, horse, cow and sheep as hosts) and satisfied all criteria of being putative targets. Additionally, we subjected these 4 proteins to virtual screening of a drug-like compound library. In all cases, molecules predicted to form favorable interactions and which showed high complementarity to the target were found among the top ranking compounds. The remaining 6 essential proteins (adk, gapA, glyA, fumC, gnd, and aspA) have homologs in the host proteomes. Their active site cavities were compared to the respective cavities in host proteins. We propose that some of these proteins can be selectively targeted using structure-based drug design approaches (SBDD). Our results facilitate the selection of C. pseudotuberculosis putative proteins for developing broad-spectrum novel drugs and vaccines. A few of the targets identified here have been validated in other microorganisms, suggesting that our modelome strategy is effective and can also be applicable to other pathogens.
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Bolaños V, Díaz-Martínez A, Soto J, Rodríguez MA, López-Camarillo C, Marchat LA, Ramírez-Moreno E. The flavonoid (-)-epicatechin affects cytoskeleton proteins and functions in Entamoeba histolytica. J Proteomics 2014; 111:74-85. [PMID: 24887480 DOI: 10.1016/j.jprot.2014.05.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 05/01/2014] [Accepted: 05/22/2014] [Indexed: 11/18/2022]
Abstract
UNLABELLED Human amoebiasis is an intestinal disease with a global distribution. Due to reports of parasite resistance or susceptibility reduction to metronidazole treatment, there is a renewed interest for the search of new molecules with antiamoebic activity. The flavonoid (-)-epicatechin that was isolated from the Mexican medicinal plant Geranium mexicanum HBK has an in vitro activity against E. histolytica trophozoites, however its molecular effects have been poorly documented. Using a proteomic approach based on two-dimensional gel electrophoresis and mass spectrometry (ESI-MS/MS) analysis, we evidenced that E. histolytica cytoskeleton proteins exhibit differential abundance in response to (-)-epicatechin treatment. Moreover, functional assays revealed modification on pathogenic mechanisms associated with cytoskeleton functionality, namely, adhesion, migration, phagocytosis and cytolysis. Consequently, these data suggested that (-)-epicatechin could affect virulence properties of this human pathogen. BIOLOGICAL SIGNIFICANCE This work contributes with some advances in the action mechanisms involved in the antiamoebic effect of the flavonoid (-)-epicatechin. We found that this flavonoid has an unusual effect on trophozoites growth that is dependent of its concentration. Additionally, we reported that (-)-epicatechin affects mainly amebic cytoskeleton proteins, which results in alteration on important virulence mechanisms, like adhesion, migration, phagocytosis and cytolysis. This study provides new knowledge about a potential alternative therapy directed to the treatment of amoebiasis.
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Affiliation(s)
- Verónica Bolaños
- Posgrado en Biomedicina Molecular, ENMyH, Instituto Politécnico Nacional, México City 07320, México
| | - Alfredo Díaz-Martínez
- Posgrado en Biomedicina Molecular, ENMyH, Instituto Politécnico Nacional, México City 07320, México
| | - Jacqueline Soto
- Posgrado en Biomedicina Molecular, ENMyH, Instituto Politécnico Nacional, México City 07320, México
| | - Mario A Rodríguez
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV-IPN, México City A.P. 14740, México
| | - Cesar López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, México City 03100, México
| | - Laurence A Marchat
- Posgrado en Biomedicina Molecular, ENMyH, Instituto Politécnico Nacional, México City 07320, México; Doctorado en Biotecnología, ENMyH, Instituto Politécnico Nacional, México City 07320, México
| | - Esther Ramírez-Moreno
- Posgrado en Biomedicina Molecular, ENMyH, Instituto Politécnico Nacional, México City 07320, México; Doctorado en Biotecnología, ENMyH, Instituto Politécnico Nacional, México City 07320, México.
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Fang Z, Tong H, Zhang S, Fang H, Lu S, Xu B. Construction of a recombinant plasmid harbouring the glyceraldenyde-3-phosphate dehydrogenase gene of periodic Brugia malayi and observation on DNA immunity. Indian J Med Microbiol 2012; 30:193-7. [PMID: 22664436 DOI: 10.4103/0255-0857.96691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
PURPOSE Controlling and eliminating lymphatic filariasis will require further research of preventative measures and implementation. Parasite is dependent on glycolysis for ATP production. The glycolytic enzyme glyceraldenyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and therefore is either a potential target for anti-parasite drug development or a vaccine candidate. Therefore, we tried to investigate the DNA vaccine-elicited immune responses in BALB/c mice. MATERIALS AND METHODS We cloned a gene encoding the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from periodic Brugia malayi into vector pcDNA3.1. Mice were injected at a dosage of 100 μg recombinant plasmid DNA with CpG intramuscular injection and immunized three times at 2-week intervals. pcDNA3.1 and normal saline were used as control. The tissue of muscles at the 4 weeks after the third injection was collected and target genes were detected using RT-PCR. The humoral responses elicited in mice by inoculation with the recombinant plasmid pcDNA3.1-BmGAPDH were detected using a standard ELISA. Two weeks after the third immunization, stimulation index (SI) was measured using the MTT method and the level of secreted IL-4 and INF-g were detected using ELISA. RESULTS Specific gene fragment coding GAPDH was amplified and the recombinant plasmid pcDNA3.1-BmGAPDH was constructed. Post-challenge sera from the mice immunized with the DNA vaccine had specific antibody titres of 1:1600 to 1:6400, and the highest titre was observed in the mice that were inoculated by pcDNA3.1-BmGAPDH/CpG at 6 weeks. At 4 weeks after immunization, the spleens of the mice were obviously enlarged. The proliferation of spleen T lymphocytes seen on the MTT assay was higher in the pcDNA3.1-BmGAPDH group than in the control group (P value <0.05). The levels of IL-4 and INF-γ in serums from the immunized mice were significantly higher than that of the control (P value <0.05). CONCLUSIONS We conclude that the recombinant eukaryotic plasmid pcDNA3.1-BmGAPDH could elicit humoral and cellular immune responses in mice.
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Affiliation(s)
- Z Fang
- Department of Parasitology, School of Basic Medical Sciences, Nantong University, Nantong, Jiangsu - 226 001, China
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Sahoo GC, Dikhit MR, Rani M, Ansari MY, Jha C, Rana S, Das P. Analysis of sequence, structure of GAPDH of Leishmania donovani and its interactions. J Biomol Struct Dyn 2012; 31:258-75. [PMID: 22830998 DOI: 10.1080/07391102.2012.698189] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Drug resistance acquired by Leishmania donovani (Ldv) is a major problem in the treatment and control of visceral leishmaniasis (VL). Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a major glycolytic enzyme has been targeted as is found in other protozoan which cause diseases like sleeping sickness. GAPDH gene of Ldv (AG83 strain) was amplified, sequenced, and modeled on the basis of crystal structure of Leishmania mexicana. The model of the Ldv GAPDH exhibited NAD-binding domain with Rossmann folding. Virtual screening of different experimentally proved compounds with the crystal and the modeled structures of GAPDH of Leishmania strains revealed diverse binding affinities of different compounds. Comparison of binding affinities (based on different programs) of compounds revealed that discovery studio v2.5 (Ligandfit) was able to predict the most hit compounds, the best hit compounds against GAPDH of Leishmania strains are hydrazine, vetrazine, and benzyl carbazate. It is predicted that patients suffering from both VL and cardiac disorders (atrial fibrillation) may benefit if they are treated with warfarin in conjunction with first-line antileishmanial therapies such as miltefosine and AmBisome.
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Affiliation(s)
- Ganesh Chandra Sahoo
- BioMedical Informatics Center, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, 800007 Patna, India.
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Hernández-Cuevas NA, Hernandez-Rivas R, Sosa-Peinado A, Rojo-Domínguez A, Vargas M. Identification and evaluation of inhibitors of the EhGEF1 protein from Entamoeba histolytica. J Mol Recognit 2012; 24:935-44. [PMID: 22038800 DOI: 10.1002/jmr.1137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The Dbl family of guanine nucleotide exchange factors (GEFs) is made up of a vast array of members that participate in the activation of the Rho family of small GTPases. Dbl-family proteins promote the exchange of guanosine diphosphate/guanosine triphosphate (GDP/GTP) in their target molecules, resulting in the activation of a variety of signaling pathways involved in diverse cellular events, such as actin-cytoskeleton remodeling, cellular invasion, cell movement, and other functions. It has been reported that members of the Dbl family have important roles in several cellular events in Entamoeba histolytica. These include activation of the actin cytoskeleton, cytokinesis, capping, uroid formation, cellular proliferation, erythrophagocytosis, cell migration, and chemotaxis. Here, we report the identification and testing of inhibitors of the E. histolytica guanine nucleotide exchange factor 1 (EhGEF1) protein (the research compounds 2BYRF, 2BY05, 2BYT6, 2BYLX, and 2BYPD), which decreased the in vitro ability of the protein to exchange GDP/GTP at its target GTPases, EhRacG and EhRho1, by 14.9-85.2%. Interestingly, the drug 1,1'-(1,2-phenylene)-bis-(1H-pyrrole-2,5-dione), which completely inhibits the GEF activity of the Trio protein in human cells, decreases the GEF activity of the EhGEF1 protein on the EhRacG and EhRho1 GTPases by 55.7% and 3.2%, respectively. The identification and evaluation of such inhibitors opens up the possibility of obtaining a new pharmacological tool to study the function of amoeba GEF proteins, their roles in various Rho GTPase-mediated signaling pathways, and the repercussions of modulating their activities with respect to several mechanisms related to E. histolytica pathogenesis.
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Affiliation(s)
- N A Hernández-Cuevas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del IPN, México DF, México
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Ramos MA, Mares RE, Magaña PD, Rivas ID, Meléndez-López SG. Entamoeba histolytica: Biochemical characterization of a protein disulfide isomerase. Exp Parasitol 2011; 128:76-81. [DOI: 10.1016/j.exppara.2011.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 02/05/2011] [Accepted: 02/08/2011] [Indexed: 11/29/2022]
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Current and future perspectives on the chemotherapy of the parasitic protozoa Trichomonas vaginalis and Entamoeba histolytica. Future Med Chem 2009; 1:619-43. [DOI: 10.4155/fmc.09.59] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Trichomonas vaginalis and Entamoeba histolytica are clinically important protozoa that affect humans. T. vaginalis produces sexually transmitted infections and E. histolytica is the causative agent of amebic dysentery. Metronidazole, a compound first used to treat T. vaginalis in 1959, is still the main drug used worldwide to treat these pathogens. It is essential to find new biochemical differences in these organisms that could be exploited to develop new antiprotozoal chemotherapeutics. Recent findings associated with T. vaginalis and E. histolytica biochemistry and host–pathogen interactions are surveyed. Knowledge concerning the biochemistry of these parasites is serving to form the foundation for the development of new approaches to control these important human pathogens.
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