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Mazandu GK, Hooper C, Opap K, Makinde F, Nembaware V, Thomford NE, Chimusa ER, Wonkam A, Mulder NJ. IHP-PING-generating integrated human protein-protein interaction networks on-the-fly. Brief Bioinform 2020; 22:5943797. [PMID: 33129201 DOI: 10.1093/bib/bbaa277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/12/2020] [Accepted: 09/21/2020] [Indexed: 01/04/2023] Open
Abstract
Advances in high-throughput sequencing technologies have resulted in an exponential growth of publicly accessible biological datasets. In the 'big data' driven 'post-genomic' context, much work is being done to explore human protein-protein interactions (PPIs) for a systems level based analysis to uncover useful signals and gain more insights to advance current knowledge and answer specific biological and health questions. These PPIs are experimentally or computationally predicted, stored in different online databases and some of PPI resources are updated regularly. As with many biological datasets, such regular updates continuously render older PPI datasets potentially outdated. Moreover, while many of these interactions are shared between these online resources, each resource includes its own identified PPIs and none of these databases exhaustively contains all existing human PPI maps. In this context, it is essential to enable the integration of or combining interaction datasets from different resources, to generate a PPI map with increased coverage and confidence. To allow researchers to produce an integrated human PPI datasets in real-time, we introduce the integrated human protein-protein interaction network generator (IHP-PING) tool. IHP-PING is a flexible python package which generates a human PPI network from freely available online resources. This tool extracts and integrates heterogeneous PPI datasets to generate a unified PPI network, which is stored locally for further applications.
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Affiliation(s)
- Gaston K Mazandu
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI-Africa WT Centre, University of Cape Town, Health Sciences Campus. Anzio Rd, Observatory, 7925, South Africa.,African Institute for Mathematical Sciences, 5-7 Melrose Road, Muizenberg, 7945, Cape Town, South Africa.,Division of Human Genetics, Department of Pathology, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa
| | - Christopher Hooper
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI-Africa WT Centre, University of Cape Town, Health Sciences Campus. Anzio Rd, Observatory, 7925, South Africa
| | - Kenneth Opap
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI-Africa WT Centre, University of Cape Town, Health Sciences Campus. Anzio Rd, Observatory, 7925, South Africa
| | - Funmilayo Makinde
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI-Africa WT Centre, University of Cape Town, Health Sciences Campus. Anzio Rd, Observatory, 7925, South Africa.,African Institute for Mathematical Sciences, 5-7 Melrose Road, Muizenberg, 7945, Cape Town, South Africa
| | - Victoria Nembaware
- Division of Human Genetics, Department of Pathology, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa
| | - Nicholas E Thomford
- Division of Human Genetics, Department of Pathology, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa.,School of Medical Sciences, University of Cape Coast, PMB, Cape Coast, Ghana
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa
| | - Nicola J Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI-Africa WT Centre, University of Cape Town, Health Sciences Campus. Anzio Rd, Observatory, 7925, South Africa
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Agamah FE, Mazandu GK, Hassan R, Bope CD, Thomford NE, Ghansah A, Chimusa ER. Computational/in silico methods in drug target and lead prediction. Brief Bioinform 2020; 21:1663-1675. [PMID: 31711157 PMCID: PMC7673338 DOI: 10.1093/bib/bbz103] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 01/10/2023] Open
Abstract
Drug-like compounds are most of the time denied approval and use owing to the unexpected clinical side effects and cross-reactivity observed during clinical trials. These unexpected outcomes resulting in significant increase in attrition rate centralizes on the selected drug targets. These targets may be disease candidate proteins or genes, biological pathways, disease-associated microRNAs, disease-related biomarkers, abnormal molecular phenotypes, crucial nodes of biological network or molecular functions. This is generally linked to several factors, including incomplete knowledge on the drug targets and unpredicted pharmacokinetic expressions upon target interaction or off-target effects. A method used to identify targets, especially for polygenic diseases, is essential and constitutes a major bottleneck in drug development with the fundamental stage being the identification and validation of drug targets of interest for further downstream processes. Thus, various computational methods have been developed to complement experimental approaches in drug discovery. Here, we present an overview of various computational methods and tools applied in predicting or validating drug targets and drug-like molecules. We provide an overview on their advantages and compare these methods to identify effective methods which likely lead to optimal results. We also explore major sources of drug failure considering the challenges and opportunities involved. This review might guide researchers on selecting the most efficient approach or technique during the computational drug discovery process.
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Affiliation(s)
- Francis E Agamah
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Gaston K Mazandu
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
- African Institute for Mathematical Sciences, Muizenberg, Cape Town 7945, South Africa
| | - Radia Hassan
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
| | - Christian D Bope
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
- Faculty of Sciences, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Nicholas E Thomford
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
- School of Medical Sciences, University of Cape Coast, PMB, Cape Coast, Ghana
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, PO Box LG 581, Legon, Ghana
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Observatory 7925, South Africa
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Akinola RO, Mazandu GK, Mulder NJ. A Quantitative Approach to Analyzing Genome Reductive Evolution Using Protein-Protein Interaction Networks: A Case Study of Mycobacterium leprae. Front Genet 2016; 7:39. [PMID: 27066064 PMCID: PMC4809885 DOI: 10.3389/fgene.2016.00039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 03/08/2016] [Indexed: 01/18/2023] Open
Abstract
The advance in high-throughput sequencing technologies has yielded complete genome sequences of several organisms, including complete bacterial genomes. The growing number of these available sequenced genomes has enabled analyses of their dynamics, as well as the molecular and evolutionary processes which these organisms are under. Comparative genomics of different bacterial genomes have highlighted their genome size and gene content in association with lifestyles and adaptation to various environments and have contributed to enhancing our understanding of the mechanisms of their evolution. Protein–protein functional interactions mediate many essential processes for maintaining the stability of the biological systems under changing environmental conditions. Thus, these interactions play crucial roles in the evolutionary processes of different organisms, especially for obligate intracellular bacteria, proven to generally have reduced genome sizes compared to their nearest free-living relatives. In this study, we used the approach based on the Renormalization Group (RG) analysis technique and the Maximum-Excluded-Mass-Burning (MEMB) model to investigate the evolutionary process of genome reduction in relation to the organization of functional networks of two organisms. Using a Mycobacterium leprae (MLP) network in comparison with a Mycobacterium tuberculosis (MTB) network as a case study, we show that reductive evolution in MLP was as a result of removal of important proteins from neighbors of corresponding orthologous MTB proteins. While each orthologous MTB protein had an increase in number of interacting partners in most instances, the corresponding MLP protein had lost some of them. This work provides a quantitative model for mapping reductive evolution and protein–protein functional interaction network organization in terms of roles played by different proteins in the network structure.
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Affiliation(s)
- Richard O Akinola
- Computational Biology Group, Department of Integrative Biomedical Sciences, Medical School, Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape Town, South Africa; Department of Mathematics, Faculty of Natural Sciences, University of JosJos, Nigeria
| | - Gaston K Mazandu
- Computational Biology Group, Department of Integrative Biomedical Sciences, Medical School, Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape Town, South Africa; African Institute for Mathematical SciencesCape Town, South Africa; African Institute for Mathematical SciencesCape Coast, Ghana
| | - Nicola J Mulder
- Computational Biology Group, Department of Integrative Biomedical Sciences, Medical School, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Cape Town, South Africa
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Information content-based Gene Ontology functional similarity measures: which one to use for a given biological data type? PLoS One 2014; 9:e113859. [PMID: 25474538 PMCID: PMC4256219 DOI: 10.1371/journal.pone.0113859] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 10/31/2014] [Indexed: 12/23/2022] Open
Abstract
The current increase in Gene Ontology (GO) annotations of proteins in the existing genome databases and their use in different analyses have fostered the improvement of several biomedical and biological applications. To integrate this functional data into different analyses, several protein functional similarity measures based on GO term information content (IC) have been proposed and evaluated, especially in the context of annotation-based measures. In the case of topology-based measures, each approach was set with a specific functional similarity measure depending on its conception and applications for which it was designed. However, it is not clear whether a specific functional similarity measure associated with a given approach is the most appropriate, given a biological data set or an application, i.e., achieving the best performance compared to other functional similarity measures for the biological application under consideration. We show that, in general, a specific functional similarity measure often used with a given term IC or term semantic similarity approach is not always the best for different biological data and applications. We have conducted a performance evaluation of a number of different functional similarity measures using different types of biological data in order to infer the best functional similarity measure for each different term IC and semantic similarity approach. The comparisons of different protein functional similarity measures should help researchers choose the most appropriate measure for the biological application under consideration.
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Magombedze G, Dowdy D, Mulder N. Latent Tuberculosis: Models, Computational Efforts and the Pathogen's Regulatory Mechanisms during Dormancy. Front Bioeng Biotechnol 2013; 1:4. [PMID: 25023946 PMCID: PMC4090907 DOI: 10.3389/fbioe.2013.00004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 08/12/2013] [Indexed: 01/07/2023] Open
Abstract
Latent tuberculosis is a clinical syndrome that occurs after an individual has been exposed to the Mycobacterium tuberculosis (Mtb) Bacillus, the infection has been established and an immune response has been generated to control the pathogen and force it into a quiescent state. Mtb can exit this quiescent state where it is unresponsive to treatment and elusive to the immune response, and enter a rapid replicating state, hence causing infection reactivation. It remains a gray area to understand how the pathogen causes a persistent infection and it is unclear whether the organism will be in a slow replicating state or a dormant non-replicating state. The ability of the pathogen to adapt to changing host immune response mechanisms, in which it is exposed to hypoxia, low pH, nitric oxide (NO), nutrient starvation, and several other anti-microbial effectors, is associated with a high metabolic plasticity that enables it to metabolize under these different conditions. Adaptive gene regulatory mechanisms are thought to coordinate how the pathogen changes their metabolic pathways through mechanisms that sense changes in oxygen tension and other stress factors, hence stimulating the pathogen to make necessary adjustments to ensure survival. Here, we review studies that give insights into latency/dormancy regulatory mechanisms that enable infection persistence and pathogen adaptation to different stress conditions. We highlight what mathematical and computational models can do and what they should do to enhance our current understanding of TB latency.
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Affiliation(s)
- Gesham Magombedze
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN, USA
| | - David Dowdy
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Nicola Mulder
- Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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Deffur A, Mulder NJ, Wilkinson RJ. Co-infection with Mycobacterium tuberculosis and human immunodeficiency virus: an overview and motivation for systems approaches. Pathog Dis 2013; 69:101-13. [PMID: 23821533 DOI: 10.1111/2049-632x.12060] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/17/2013] [Accepted: 06/20/2013] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis is a devastating disease that accounts for a high proportion of infectious disease morbidity and mortality worldwide. HIV-1 co-infection exacerbates tuberculosis. Enhanced understanding of the host-pathogen relationship in HIV-1 and Mycobacterium tuberculosis co-infection is required. While reductionist approaches have yielded many valuable insights into disease pathogenesis, systems approaches are required that develop data-driven models able to predict emergent properties of this complex co-infection system in order to develop novel therapeutic approaches and to improve diagnostics. Here, we provide a pathogenesis-focused overview of HIV-TB co-infection followed by an introduction to systems approaches and concrete examples of how such approaches are useful.
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Affiliation(s)
- Armin Deffur
- Clinical Infectious Diseases Research Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Department of Medicine, University of Cape Town, Cape Town, South Africa
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Rapanoel HA, Mazandu GK, Mulder NJ. Predicting and analyzing interactions between Mycobacterium tuberculosis and its human host. PLoS One 2013; 8:e67472. [PMID: 23844013 PMCID: PMC3699628 DOI: 10.1371/journal.pone.0067472] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 05/17/2013] [Indexed: 12/20/2022] Open
Abstract
The outcome of infection by Mycobacterium tuberculosis (Mtb) depends greatly on how the host responds to the bacteria and how the bacteria manipulates the host, which is facilitated by protein-protein interactions. Thus, to understand this process, there is a need for elucidating protein interactions between human and Mtb, which may enable us to characterize specific molecular mechanisms allowing the bacteria to persist and survive under different environmental conditions. In this work, we used the interologs method based on experimentally verified intra-species and inter-species interactions to predict human-Mtb functional interactions. These interactions were further filtered using known human-Mtb interactions and genes that are differentially expressed during infection, producing 190 interactions. Further analysis of the subcellular location of proteins involved in these human-Mtb interactions confirms feasibility of these interactions. We also conducted functional analysis of human and Mtb proteins involved in these interactions, checking whether these proteins play a role in infection and/or disease, and enriching Mtb proteins in a previously predicted list of drug targets. We found that the biological processes of the human interacting proteins suggested their involvement in apoptosis and production of nitric oxide, whereas those of the Mtb interacting proteins were relevant to the intracellular environment of Mtb in the host. Mapping these proteins onto KEGG pathways highlighted proteins belonging to the tuberculosis pathway and also suggested that Mtb proteins might use the host to acquire nutrients, which is in agreement with the intracellular lifestyle of Mtb. This indicates that these interactions can shed light on the interplay between Mtb and its human host and thus, contribute to the process of designing novel drugs with new biological mechanisms of action.
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Affiliation(s)
- Holifidy A. Rapanoel
- Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Gaston K. Mazandu
- Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Nicola J. Mulder
- Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- * E-mail:
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Magombedze G, Mulder N. Understanding TB latency using computational and dynamic modelling procedures. INFECTION GENETICS AND EVOLUTION 2012; 13:267-83. [PMID: 23146828 DOI: 10.1016/j.meegid.2012.09.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 07/31/2012] [Accepted: 09/25/2012] [Indexed: 12/26/2022]
Abstract
The Mycobacterium tuberculosis bacilli's potency to cause persistent latent infection that is unresponsive to the current cocktail of TB drugs is strongly associated with its ability to adapt to changing intracellular environments, and tolerating, evading and subverting host defence mechanisms. We applied a combination of bioinformatics and mathematical modelling methods to enhance the understanding of TB latency dynamics. Analysis of time course microarray gene expression data was carried out and gene profiles for bacilli adaptation and survival in latency, simulated by hypoxia were determined. Reverse network engineering techniques were used to predict gene dependencies and regulatory interactions. Biochemical systems theory was applied to mathematically model the inferred gene regulatory networks. Significant regulatory genes involved in latency were determined by a combination of systems biology procedures and mathematical modelling of the inferred regulatory networks. Analysis of gene clusters of the inferred networks in the stationary and non-replicating phases of the bacilli predicted probable functions of some of the latency genes to be associated with latency genes of known functions. The systems biology approach and mathematical computational deletion experiments predicted key genes in the TB latency/dormancy program that may be possible TB drug targets. However, these gene candidates require experimental testing and validation.
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Affiliation(s)
- Gesham Magombedze
- National Institute for Mathematical and Biological Synthesis, 1534 White Ave., University of Tennessee, Knoxville, TN 37996-1527, USA.
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