ABSTRACT
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a global pandemic. Viral entry into host cells is mediated by spike glycoprotein (SGP) interactions with angiotensin-converting enzyme 2 (ACE2) and heparan sulfate glycosaminoglycans on the cell surface. Carbohydrate small molecules were found to bind to the receptor binding domain (RBD) of SGP, which also interacts with ACE2, forming a ternary complex. Moreover, glycans isolated from sea cucumber and red alga species exhibited anti-SARS-CoV-2 activities, presumably by blocking viral entry mediated through SGP-heparan sulfate interactions. Here we report a collection of computational studies conducted as part of a collaborative effort to investigate the effects of marine natural products (NPs) on the wild-type and N501Y mutant SGP RBD. Starting from an X-ray crystal structure of the RBD-ACE2 complex, a model of SGP RBD was built. To investigate the static and dynamic behavior of RBD-NP interactions, blind and site-targeted molecular docking using diverse docking programs (Glide, AutoDock Vina or ClusPro) was carried out, followed by extensive molecular dynamics simulations with two force fields (CHARMM36 or Glycam06) and binding free energy calculations. Predicted conformations of the NPs varied considerably when modeled in water or in complex with RBD. Five NP binding sites on the RBD were studied. NP binding specificities towards SARS-CoV-2 variants were explained and important RBD residues were identified. Statistical analyses of the stability of various protein-NP complexes during molecular dynamics simulations helped to differentiate pseudo-vs. real-binding sites. Our results provide significant insights into the importance of extensive molecular dynamics calculations in order to move beyond the limitations of molecular docking.
ABSTRACT
RATIONALE4,4-44,4% of children suffer from post-COVID syndrome, commonly known as long- COVID, after an acute SARS-CoV-2 infection. However, an uniform clinical definition, and guidelines to diagnose or treat children suspected of long-COVID are lacking. Multiple careprograms have been initiated worldwide. In this study, we aimed to assess the currently available pediatric international long-COVID care programs and explore the characteristics of their patient cohorts.METHODSWe established an international network (IP4C) and performed a crosssectional analysis from aggregated data collected by its members using a survey. Topics included: the used definition for long-covid in children, the organization of pediatric long-COVID clinics and long-COVID patients characteristics. Descriptive analysis of the aggregated data was used to summarize and compare each of these categories across countries. RESULTSWe included data concerning organization of care from 17 cohorts based in 13 different countries. A wide range of definitions for long COVID was used, which differed mostly in duration of symptoms and the necessity of microbiologically proven SARS-COV-2 infection. 66,6-100% of patients in the long- COVID cohorts suffered from complaints for more than twelve weeks, and 49,5-97,3% of patients had a positive RT-PCR or serology for SARS-CoV-2. Most long-COVID care programs consisted of real-life visits with multidisciplinary teams, consisting of general pediatricians, pediatric lung specialists, cardiologists and infectiologist, a physiotherapist and psychologist. The type of investigations performed at the long-COVID clinics ranged from assessment of medical history (100%) and standardized questionnaires (91%) to in depth evaluation of organ functioning (e.g. spirometry performed in 0-100% of patients). Aggregated data of 431 long-COVID patients from 11 dedicated long-COVID care programs were analyzed. Mean age of patients ranged from 6,5-16,4 years old. Girls were overrepresented in most cohorts (20-65%). 28-81,8% of patient had a positive medical history, most commonly atopic syndrome, asthma and prematurity. Most patients (90- 100%) suffered from asymptomatic or mild acute COVID-19. Frequent long-COVID symptoms were fatigue, headaches, concentration difficulties, dyspnea and sleep disturbances. 5-37% of patients had severe limitations in daily life. CONCLUSIONSThis is the first study to describe the organization of pediatric long-COVID care. It demonstrates that pediatric long-COVID is recognized worldwide as a multisystemic disease, but its definition and care programs for pediatric long- COVID patients differ between cohorts. A clear definition of pediatric long-COVID is needed to improve international scientific collaboration and patient care. Our international network will facilitate further collaboration in investigation pathophysiology and therapeutic interventions in order to provide evidence based medical care for these patients.