Targeting the glycans: A paradigm for host-targeted and COVID-19 drug design

Blood Features Associated with Viral Infection Severity: An Experience from COVID-19-Pandemic Patients Hospitalized in the Center of Iran, Yazd

Pandemics such as coronavirus disease 2019 (COVID-19) can manifest as systemic infections that affect multiple organs and show laboratory manifestations. We aimed to analyze laboratory findings to understand possible mechanisms of organ dysfunction and risk stratification of hospitalized patients in these epidemics. Methods. This retrospective study was conducted among patients admitted to COVID-19 referral treatment center, Shahid Sadoughi Hospital, Yazd, Iran, from April 21 to November 21, 2021. It was the fifth peak of COVID-19 in Iran, and Delta (VOC-21APR-02; B.1-617.2) was the dominant and most concerning strain. All cases were positive for COVID-19 by RT-PCR test. Lab information of included patients and association of sex, age, and outcome were analyzed, on admission. Results. A total of 466 COVID-19 patients were included in the study, the majority of whom were women (68.9%). The average age of hospitalized patients in male and female patients was 57.68 and 41.32 years, respectively (p < 0.01). During hospitalization, abnormality in hematological and biochemical parameters was significant and was associated with the outcome of death in patients. There was incidence of lymphopenia, neutrophilia, anemia, and thrombocytopenia. The changes in neutrophil/lymphocyte (N/L) and hematocrit/albumin (Het/Alb) ratio and potassium and calcium levels were significant. Conclusion. Based on these results, new biochemical and hematological parameters can be used to predict the spread of infection and the underlying molecular mechanism. Viral infection may spread through blood cells and the immune system.

Harnessing the power of mollusc lectins as immuno-protective biomolecules

The rapid advancement of molecular research on macromolecules has contributed to the discovery of 'Lectin', a carbohydrate-binding protein which specifically interacts with receptors on the surface of glycans and regulates various cellular activities thereby stimulating immunological functions. Considering the wide variety of sources and immunological significance, research has led to the discovery of lectins in invertebrate molluscs. Such lectins in molluscs mediate active immune response as they lack adaptive immunity. Phylum Mollusca is identified with different types of lectins such as C-lectin, Galectin, P-lectin, I-lectin, and H-lectin, along with other immunologically significant lectin molecules such as F- lectin, R-lectin, ficolins, chitinase like lectin etc., all of these with specific ligand binding and structural diversity. Molluscan C-type lectins are the most functional ones that increase the activity of phagocytic cells through specific carbohydrate binding of antigenic ligands and haemocyte adhesion thereby enhancing the immune response. Helix pomatia agglutinin and Helix aspersa agglutinin are the two H-lectins that were identified within molluscs that could even target cancer-progressing cells through specific binding. Also, these lectins identified in molluscs are proven to be efficient in antibacterial and immunomodulatory functions. These insights attract researchers to identify novel lectins in molluscs and their characterization that play a key role in protection against diseases. This review discusses the structural features of mollusc lectins, their specific binding, molecular interactions and their immunological applications.

Targeting SARS-CoV-2 entry processes: The promising potential and future of host-targeted small-molecule inhibitors

The COVID-19 pandemic, caused by SARS-CoV-2, has had a huge impact on global health. To respond to rapidly mutating viruses and to prepare for the next pandemic, there is an urgent need to develop small molecule therapies that target critical stages of the SARS-CoV-2 life cycle. Inhibiting the entry process of the virus can effectively control viral infection and play a role in prevention and treatment. Host factors involved in this process, such as ACE2, TMPRSS2, ADAM17, furin, PIKfyve, TPC2, CTSL, AAK1, V-ATPase, HSPG, and NRP1, have been found to be potentially good targets with stability. Through further exploration of the cell entry process of SARS-CoV-2, small-molecule drugs targeting these host factors have been developed. This review focuses on the structural functions of potential host cell targets during the entry of SARS-CoV-2 into host cells. The research progress, chemical structure, structure-activity relationship, and clinical value of small-molecule inhibitors against COVID-19 are reviewed to provide a reference for the development of small-molecule drugs against COVID-19.

Seasonal effects decouple SARS-CoV-2 haplotypes worldwide

Background: Variants of concern (VOCs) have been replacing each other during the still rampant COVID-19 pandemic. As a result, SARS-CoV-2 populations have evolved increasingly intricate constellations of mutations that often enhance transmissibility, disease severity, and other epidemiological characteristics. The origin and evolution of these constellations remain puzzling. Methods: Here we study the evolution of VOCs at the proteome level by analyzing about 12 million genomic sequences retrieved from GISAID on July 23, 2022. A total 183,276 mutations were identified and filtered with a relevancy heuristic. The prevalence of haplotypes and free-standing mutations was then tracked monthly in various latitude corridors of the world. Results: A chronology of 22 haplotypes defined three phases driven by protein flexibility-rigidity, environmental sensing, and immune escape. A network of haplotypes illustrated the recruitment and coalescence of mutations into major VOC constellations and seasonal effects of decoupling and loss. Protein interaction networks mediated by haplotypes predicted communications impacting the structure and function of proteins, showing the increasingly central role of molecular interactions involving the spike (S), nucleocapsid (N), and membrane (M) proteins. Haplotype markers either affected fusogenic regions while spreading along the sequence of the S-protein or clustered around binding domains. Modeling of protein structure with AlphaFold2 showed that VOC Omicron and one of its haplotypes were major contributors to the distortion of the M-protein endodomain, which behaves as a receptor of other structural proteins during virion assembly. Remarkably, VOC constellations acted cooperatively to balance the more extreme effects of individual haplotypes. Conclusions: Our study uncovers seasonal patterns of emergence and diversification occurring amid a highly dynamic evolutionary landscape of bursts and waves. The mapping of genetically-linked mutations to structures that sense environmental change with powerful ab initio modeling tools demonstrates the potential of deep-learning for COVID-19 predictive intelligence and therapeutic intervention.

The emergence of SARS-CoV-2 variants of concern in Australia by haplotype coalescence reveals a continental link to COVID-19 seasonality

SARS-CoV-2 continues to evolve, even after implementation of public-wide vaccination, as can be observed by an increasing number of mutations over time. Compared to responses by the United States and European countries, the disease mitigation strategies employed by the Australian government have been swift and effective. This provides a unique opportunity to study the emergence of variants of concern (VOCs) at many latitude levels in a country that has been able to control infection for the majority of the pandemic. In the present study, we explored the occurrence and accumulation of major mutations typical of VOCs in different regions of Australia and the effects that latitude has on the establishment of VOC-induced disease. We also studied the constellation of mutations characteristic of VOCs to determine if the mutation sets acted as haplotypes. Our goal was to explore processes behind the emergence of VOCs as the viral disease progresses towards becoming endemic. Most reported COVID-19 cases were in largest cities located within a -30°S to - 50°S latitude corridor previously identified to be associated with seasonal behavior. Accumulation plots of individual amino acid variants of major VOCs showed that the first major haplotypes reported worldwide were also present in Australia. A classification of accumulation plots revealed the existence of 18 additional haplotypes associated with VOCs alpha, delta and omicron. Core mutant constellations for these VOCs and curve overlaps for variants in each set of haplotypes demonstrated significant decoupling patterns, suggesting processes of emergence. Finally, construction of a "haplotype network" that describes the viral population landscape of Australia throughout the COVID-19 pandemic revealed significant and unanticipated seasonal patterns of emergence and diversification. These results provide a unique window into our evolutionary understanding of a human pathogen of great significance. They may guide future research into mitigation and prediction strategies for future VOCs.

Malaria Epidemiology and COVID-19 Pandemic: Are They Interrelated?

Coronavirus disease 2019 (COVID-19) is a systemic disease, impacting multiple organs in the human body. But COVID-19 also impacts other diseases of relevance to public and planetary health. To understand and respond to the COVID-19 pandemic, we need an intersectional conceptual lens and systems thinking. For example, the strain on health care systems due to COVID-19 has adversely impacted global malaria elimination programs. With many epidemiological, clinical, and biological parallels documented, we examined in this study the scenario of malaria and COVID-19 syndemic in India. The disruptive influence of COVID-19 on the National Framework for Malaria Elimination (NFME), impact of unintended chemoprophylaxis, population genetic influences, and the shifting patterns of epidemiology are compared. Importantly, a time series analysis forecasted the burden of malaria increasing in the upcoming years. Although reported malaria cases showed a decline in 2020 compared to the previous years, an increase in cases was documented in 2021, with nine states reporting an increase up to July 2021. Pandemics often cause crosscutting disruptions in health care. Reshaping the priorities of the malaria elimination program and a diligent implementation of the priorities in the NFME would, therefore, be well-advised: (1) vector control, (2) antimalarial therapy recommendations, (3) monitoring drug resistance, (4) prevention of the spread of asymptomatic disease-causing low-density transmission, and (5) large-scale testing measures. In conclusion, the findings from the present study inform future comparative studies in other world regions to better understand the broader, systemic, temporal, and spatial impacts of the COVID-19 pandemic on existing and future diseases across public health systems and services.

Targeting the glycans: A paradigm for host-targeted and COVID-19 drug design

There is always a need for new approaches for the control of virus burdens caused by seasonal outbreaks, the emergence of novel viruses with pandemic potential and the development of resistance to current antiviral drugs. The outbreak of the 2019 novel coronavirus-disease COVID-19 represented a pandemic threat and declared a public health emergency of international concern. Herein, the role of glycans for the development of new drugs or vaccines, as a host-targeted approach, is discussed where may provide a front-line prophylactic or threats to protect against the current and any future respiratory-infecting virus and possibly against other respiratory pathogens. As a prototype, the role of glycans in the coronavirus infection, as well as, galectins (Gal) as the glycan-recognition agents (GRAs) in drug design are here summarized. Galectins, in particular, Gal-1 and Gal-3 are ubiquitous and important to biological systems, whose interactions with viral glycans modulate host immunity and homeostatic balance.