DNA-based microarray studies in visceral leishmaniasis: identification of biomarkers for diagnostic, prognostic and drug target for treatment

Correlated Hybrid DNA Structures Explored by the oxDNA Model

Thermodynamically, perfect DNA hybridization can be formed between probes and their corresponding targets due to the favorable energy. However, this is not the case dynamically. Here, we use molecular dynamics (MD) simulations based on the oxDNA model to investigate the process of DNA microarray hybridization. In general, correlated hybrid DNA structures are formed, including one probe associated with several targets as well as one target hybrid with multiple probes leading to the target-mediated hybridization. The formation of these two types of correlated structures largely depends on the surface coverage of the DNA microarray. Moreover, DNA sequence, DNA length, and spacer length have an impact on the structural formation. Our findings shed light on the dynamics of DNA hybridization, which is important for the application of DNA microarray.

Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays

Microarrays are one of the trailblazing technologies of the last two decades and have displayed their importance in all the associated fields of biology. They are widely explored to screen, identify, and gain insights on the characteristics traits of biomolecules (individually or in complex solutions). A wide variety of biomolecule-based microarrays (DNA microarrays, protein microarrays, glycan microarrays, antibody microarrays, peptide microarrays, and aptamer microarrays) are either commercially available or fabricated in-house by researchers to explore diverse substrates, surface coating, immobilization techniques, and detection strategies. The aim of this review is to explore the development of biomolecule-based microarray applications since 2018 onwards. Here, we have covered a different array of printing strategies, substrate surface modification, biomolecule immobilization strategies, detection techniques, and biomolecule-based microarray applications. The period of 2018–2022 focused on using biomolecule-based microarrays for the identification of biomarkers, detection of viruses, differentiation of multiple pathogens, etc. A few potential future applications of microarrays could be for personalized medicine, vaccine candidate screening, toxin screening, pathogen identification, and posttranslational modifications.

Nanomedicine in leishmaniasis: A promising tool for diagnosis, treatment and prevention of disease - An update overview

Leishmaniasis is a neglected tropical disease that has a wide spectrum of clinical manifestations, ranging from visceral to cutaneous, with millions of new cases and thousands of deaths notified every year. The severity of the disease and its various clinical forms are determined by the species of the causative agent, Leishmania, as well as the host's immune response. Major challenges still exist in the diagnosis and treatment of leishmaniasis, and there is no vaccine available to prevent this disease in humans. Nanotechnology has emerged as a promising tool in a variety of fields. In this review, we highlight the main and most recent advances in nanomedicine to improve the diagnosis and treatment, as well as for the development of vaccines, for leishmaniasis. Nanomaterials are nanometric in size and can be produced by a variety of materials, including lipids, polymers, ceramics, and metals, with varying structures and morphologies. Nanotechnology can be used as biosensors to detect antibodies or antigens, thus improving the sensitivity and specificity of such immunological and molecular diagnostic tests. While in treatment, nanomaterials can act as drug carriers or, be used directly, to reduce any toxic effects of drug compounds to the host and to be more selective towards the parasite. Furthermore, preclinical studies show that different nanomaterials can carry different Leishmania antigens, or even act as adjuvants to improve a Th1 immune response in an attempt to produce an effective vaccine.

The Geographical Distribution of Human Cutaneous and Visceral Leishmania Species Identified by Molecular Methods in Iran: A Systematic Review With Meta-Analysis

Leishmaniasis is one of the most common vector-borne parasitic diseases in Iran. Leishmania species identification is necessary for epidemiological aspects, precise prognosis, control and treatment of the disease. We systematically searched all the studies, reports, and documentation related to species identification and geographical distribution of causative agents of cutaneous (CL), mucosal (ML), and visceral leishmaniasis (VL) using DNA-based molecular diagnostic techniques in Iran. International databases including PubMed, ScienceDirect, Embase, Google Scholar, Scopus, and Web of Science were systemically searched for English articles and Iran's databases including SID, IranMedex and Magiran were searched for Persian reports and articles. Searches were performed from 1999 to 2019 (20 years). The current review was conducted using the keywords: cutaneous leishmaniasis, visceral leishmaniasis, Leishmania species, Human, Molecular, PCR, and Iran. The study quality was evaluated using the NOS checklist. This meta-analysis procedure was accomplished using STATA, version 2.7.9. Of the 3,426 records identified in the initial search, 154 articles met inclusion criteria and qualified for the systematic review and meta-analysis. In subgroup analysis, the pooled frequency of causative agents of CL isolates was 67.3% (95% CI: 59.51–74.67%) for L. major and 32.1% (95% CI: 24.72–39.87%) for L. tropica. In addition, the pooled frequency of causative agents of VL isolates was 97.1% (95% CI: 94.6–98.8%) for L. infantum and 2.9% (95% CI: 1.12–5.37%) for L. tropica. The findings of this study showed that the main causative agents of CL and VL in Iran are L. major and L. infantum, respectively. Moreover, kinetoplast DNA (kDNA) and internal transcriber spacer (ITS) were the most used markers for identifying Leishmania species. The current study provides valuable data to encourage and direct researchers as well as public health managers in the comprehensive leishmaniasis control and prevention planning in Iran.

Functional metabolomics innovates therapeutic discovery of traditional Chinese medicine derived functional compounds

Traditional Chinese medicines (TCMs) produce chemically diverse functional compounds that are importantly chemical resource for facilitating new drug discovery and development against a diversity of diseases. However, modern exploration of TCM derived functional compounds is significantly hindered by the inefficient elucidation of pharmacological functions over past decades, because conventional research methods are incapable of efficiently elucidating therapeutic potential of TCM conferred by multiple functional compounds. Functional metabolomics has the priority-capacity to characterize systems therapeutic actions of TCM by precisely capturing molecular interactions between disease response metabolite biomarkers (DRMB) and functional compounds (secondary metabolites), which underline pharmacological efficiency and associated therapeutic mechanisms. In this critical review, we innovatively summarize systems therapeutic feature of TCM derived functional compounds from a functional-metabolism perspective, then systems metabolic targets (SMT) identified by functional metabolomics method are strategically proposed to better understanding of therapeutic discovery of TCM derived functional compounds. In addition, we propose the perspective strategy as Spatial Temporal Operative Real Metabolomics (STORM) to considerably improve analytical capacity of functional metabolomics method by selectively incorporating the cutting edge technologies of mass spectrometry imaging, isotope-metabolic fluxomics, synthetic and biosynthetic chemistry, which could considerably enhance the precision and resolution of elucidating pharmacological efficiency and associated therapeutic mechanisms of TCM derived functional compounds. Collectively, such critical review is expected to provide novel perspective-strategy that could significantly improve modern exploration and exploitation of TCM derived functional compounds that further promote new drug discovery and development against the complex diseases.

DDX3 DEAD-box RNA helicase (Hel67) gene disruption impairs infectivity of Leishmania donovani and induces protective immunity against visceral leishmaniasis

Visceral leishmaniasis (VL) is a vector-borne disease caused by the digenetic protozoan parasite Leishmania donovani complex. So far there is no effective vaccine available against VL. The DDX3 DEAD-box RNA Helicase (Hel67) is 67 kDa protein which is quite essential for RNA metabolism, amastigote differentiation, and infectivity in L. major and L. infantum. To investigate the role of Hel67 in the L. donovani, we created L. donovani deficient in the Hel67. Helicase67 null mutants (LdHel67^-/-) were not able to differentiate as axenic amastigotes and were unable to infect the hamster. So, we have analyzed the prophylactic efficacy of the LdHel67^-/- null mutant in hamsters. The LdHel67^-/- null mutant based candidate vaccine exhibited immunogenic response and a higher degree of protection against L. donovani in comparison to the infected control group. Further, the candidate vaccine displayed antigen-specific delayed-type hypersensitivity (DTH) as well as strong antibody response and NO production which strongly correlates to long term protection of candidate vaccine against the infection. This study confirms the potential of LdHel67^-/- null mutant as a safe and protective live attenuated vaccine candidate against visceral leishmaniasis.

Genetically modified live attenuated vaccine: A potential strategy to combat visceral leishmaniasis

Visceral leishmaniasis (VL) is caused by a protozoan parasite Leishmania donovani mainly influencing the population of tropical and subtropical regions across the globe. The arsenal of drugs available is limited, and prolonged use of such drugs makes parasite to become resistant. Therefore, it is very imperative to develop a safe, cost-effective and inexpensive vaccine against VL. Although in recent years, many strategies have been pursued by researchers, so far only some of the vaccine candidates reached for clinical trial and more than half of them are still in pipeline. There is now a broad consent among Leishmania researchers that the perseverance of parasite is very essential for eliciting a protective immune response and may perhaps be attained by live attenuated parasite vaccination. For making a live attenuated parasite, it is very essential to ensure that the parasite is deficient of virulence and should further study genetically modified parasites to perceive the mechanism of pathogenesis. So it is believed that in the near future, a complete understanding of the Leishmania genome will explore clear strategies to discover a novel vaccine. This review describes the need for a genetically modified live attenuated vaccine against VL, and obstacles associated with its development.