A molecular dynamics simulation study of the ACE2 receptor with screened natural inhibitors to identify novel drug candidate against COVID-19.

BACKGROUND & OBJECTIVES: The massive outbreak of Novel Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) has turned out to be a serious global health issue worldwide. Currently, no drugs or vaccines are available for the treatment of COVID-19. The current computational study was attempted to identify a novel therapeutic inhibitor against novel SARS-CoV-2 using in silico drug discovery pipeline. METHODS: In the present study, the human angiotensin-converting enzyme 2 (ACE2) receptor was the target for the designing of drugs against the deadly virus. The 3D structure of the receptor was modeled & validated using a Swiss-model, Procheck & Errat server. A molecular docking study was performed between a group of natural & synthetic compounds having proven anti-viral activity with ACE2 receptor using Autodock tool 1.5.6. The molecular dynamics simulation study was performed using Desmond v 12 to evaluate the stability and interaction of the ACE2 receptor with a ligand. RESULTS: Based on the lowest binding energy, confirmation, and H-bond interaction, cinnamic acid (-5.20 kcal/mol), thymoquinone (-4.71 kcal/mol), and andrographolide (Kalmegh) (-4.00 kcal/mol) were screened out showing strong binding affinity to the active site of ACE2 receptor. MD simulations suggest that cinnamic acid, thymoquinone, and andrographolide (Kalmegh) could efficiently activate the biological pathway without changing the conformation in the binding site of the ACE2 receptor. The bioactivity and drug-likeness properties of compounds show their better pharmacological property and safer to use. INTERPRETATION & CONCLUSIONS: The study concludes the high potential of cinnamic acid, thymoquinone, and andrographolide against the SARS-CoV-2 ACE2 receptor protein. Thus, the molecular docking and MD simulation study will aid in understanding the molecular interaction between ligand and receptor binding site, thereby leading to novel therapeutic intervention.

QSAR modeling and docking analysis of D2 receptor with known olanzapine derivatives.

Dopamine (D2) receptors are known drug targets for various antipsychotics used in Schizophrenia. Therefore, it is of interest to analyze the binding features of D2 receptors with known olanzapine derivatives for further consideration using molecular docking and QSAR analysis. A 2D QSAR model was built using energy-based descriptors generated by docking as independent variable and known Ki value of Olanzapine derivatives with D2 Receptor as dependent variable. QSAR model provided coefficient of determination of r2 of 0.7 in multiple linear regression analysis. The predictive performance of QSAR model was assessed using different cross-validation procedures. Thus, data shows that a ligand-receptor binding interaction for D2 Receptor using a QSAR model is promising approach to design novel and potent inhibitors of D2 Receptor.

Functional association between NUCKS1 gene and Parkinson disease: A potential susceptibility biomarker.

Several Genome Wide Association Studies (GWASs) have reported that PARK16 gene locus possibly regulate the risk of Parkinson's disease (PD). It contains functionally interesting candidate genes for PD, regulated by number of SNPs. In present study rs823093 polymorphism in NUCKS1 gene has been evaluated as significant performer in PD though its mechanism is not yet known. Here various regulatory and functional analyses were performed using computational tools and information from databases. The rs823093 variant was predicted to locate in enhancer histone marks in blood and have strong transcription in various parts of brain, heart, kidney and liver. PhenoScanner (a database of human genotype-phenotype associations) identified significant associations of this variant with many other diseases and phenotypic conditions as well. Gene expression analysis shows significant association with multiple human tissues and multiple genes together with NUCKS1. Further, the post mortem brain samples showed diverse expressions of NUCKS1 gene in PD patients compared to healthy samples. Besides, the metabolite analysis shows significant association with serotonin a known neurotransmitter, and other 15 metabolites. In addition, NUCKS1 also showed co-expression with ZNF43 and PLIN1 genes involved in cell cycle regulation presume their association in PD. Thus, these data links NUCKS1 gene as a potential disease susceptibility biomarker for PD.

Biomarkers for detection, prognosis and therapeutic assessment of neurological disorders.

Neurological disorders have aroused a significant concern among the health scientists globally, as diseases such as Parkinson's, Alzheimer's and dementia lead to disability and people have to live with them throughout the life. Recent evidence suggests that a number of environmental chemicals such as pesticides (paraquat) and metals (lead and aluminum) are also the cause of these diseases and other neurological disorders. Biomarkers can help in detecting the disorder at the preclinical stage, progression of the disease and key metabolomic alterations permitting identification of potential targets for intervention. A number of biomarkers have been proposed for some neurological disorders based on laboratory and clinical studies. In silico approaches have also been used by some investigators. Yet the ideal biomarker, which can help in early detection and follow-up on treatment and identifying the susceptible populations, is not available. An attempt has therefore been made to review the recent advancements of in silico approaches for discovery of biomarkers and their validation. In silico techniques implemented with multi-omics approaches have potential to provide a fast and accurate approach to identify novel biomarkers.

Roles of quorum sensing molecules from Rhizobium etli RT1 in bacterial motility and biofilm formation

ABSTRACT Strain RT1 was isolated from root nodules of Lens culinaris (a lentil) and characterized as Rhizobium etli (a Gram-negative soil-borne bacterium) by 16S rDNA sequencing and phylogenetic analysis. The signaling molecules produced by R. etli (RT1) were detected and identified by high-performance liquid chromatography coupled with mass spectrometry. The most abundant and biologically active N-acyl homoserine lactone molecules (3-oxo-C8-HSL and 3-OH-C14-HSL) were detected in the ethyl acetate extract of RT1. The biological role of 3-oxo-C8-HSL was evaluated in RT1. Bacterial motility and biofilm formation were affected or modified on increasing concentrations of 3-oxo-C8-HSL. Results confirmed the existence of cell communication in RT1 mediated by 3-oxo-C8-HSL, and positive correlations were found among quorum sensing, motility and biofilm formation in RT1.

Roles of quorum sensing molecules from Rhizobium etli RT1 in bacterial motility and biofilm formation.

Strain RT1 was isolated from root nodules of Lens culinaris (a lentil) and characterized as Rhizobium etli (a Gram-negative soil-borne bacterium) by 16S rDNA sequencing and phylogenetic analysis. The signaling molecules produced by R. etli (RT1) were detected and identified by high-performance liquid chromatography coupled with mass spectrometry. The most abundant and biologically active N-acyl homoserine lactone molecules (3-oxo-C8-HSL and 3-OH-C14-HSL) were detected in the ethyl acetate extract of RT1. The biological role of 3-oxo-C8-HSL was evaluated in RT1. Bacterial motility and biofilm formation were affected or modified on increasing concentrations of 3-oxo-C8-HSL. Results confirmed the existence of cell communication in RT1 mediated by 3-oxo-C8-HSL, and positive correlations were found among quorum sensing, motility and biofilm formation in RT1.

HDVDB: a data warehouse for hepatitis delta virus.

Hepatitis Delta Virus (HDV) is an RNA virus and causes delta hepatitis in humans. Although a lot of data is available for HDV, but retrieval of information is a complicated task. Current web database 'HDVDB' provides a comprehensive web-resource for HDV. The database is basically concerned with basic information about HDV and disease caused by this virus, genome structure, pathogenesis, epidemiology, symptoms and prevention, etc. Database also supplies sequence data and bibliographic information about HDV. A tool 'siHDV Predict' to design the effective siRNA molecule to control the activity of HDV, is also integrated in database. It is a user friendly information system available at public domain and provides annotated information about HDV for research scholars, scientists, pharma industry people for further study.

Interaction between shrimp and white spot syndrome virus through PmRab7-VP28 complex: an insight using simulation and docking studies.

White spot disease is a devastating disease of shrimp Penaeus monodon in which the shrimp receptor protein PmRab7 interacts with viral envelop protein VP28 to form PmRab7-VP28 complex, which causes initiation of the disease. The molecular mechanism implicated in the disease, the dynamic behavior of proteins as well as interaction between both the biological counterparts that crafts a micro-environment feasible for entry of virus into the shrimp is still unknown. In the present study, we applied molecular modeling (MM), molecular dynamics (MD) and docking to compute surface mapping of infective amino acid residues between interacting proteins. Our result showed that α-helix of PmRab7 (encompassing Ser74, Ile143, Thr184, Arg53, Asn144, Thr184, Arg53, Arg79) interacts with ß-sheets of VP28 (containing Ser74, Ile143, Thr184, Arg53, Asn144, Thr184, Arg53, Arg79) and Arg69-Ser74, Val75-Ile143, Leu73-Ile143, Arg79-Asn144, Ala198-Ala182 bonds contributed in the formation of PmRab7-VP28 complex. Further studies on the amino acid residues and bonds may open new possibilities for preventing PmRab7-VP28 complex formation, thus reducing chances of WSD. The quantitative predictions provide a scope for experimental testing in future as well as endow with a straightforward evidence to comprehend cellular mechanisms underlying the disease.

Design of potential siRNA molecules for hepatitis delta virus gene silencing.

Hepatitis D is a liable reason of mortality and morbidity worldwide. It is caused by an RNA virus known as Hepatitis Delta Virus (HDV). Genetic studies of HDV have shown that delta antigen protein is responsible for replication of genome and play a foremost role in viral infection. Therefore, delta antigen protein may be used as suitable target for disease diagnosis. Viral activity can be restrained through RNA interference (RNAi) technology, an influential method for post transcriptional gene silencing in a sequence specific manner. However, there is a genetic variability in different viral isolates; it is a great challenge to design potential siRNA molecules which can silence the respective target genes rather than any other viral gene simultaneously. In current study two effective siRNA molecules for silencing of HDV were rationally designed and validated using computational methods, which may lead to knockdown the activity of virus. Thus, this approach may provide an insight for the chemical synthesis of antiviral RNA molecule for the treatment of hepatitis D, at genome level.

Association of 25 bp deletion in MYBPC3 gene with left ventricle dysfunction in coronary artery disease patients.

RATIONALE: Mutations in MYBPC3 encoding cardiac myosin binding protein C are common genetic cause of hereditary cardiac myopathies. An intronic 25-bp deletion in MYBPC3 at 3' region is associated with dilated (DCM) and hypertrophic (HCM) cardiomyopathies in Southeast Asia. However, the frequency of MYBPC3 25 bp deletion and associated clinical presentation has not been established in an unrelated cohort of left ventricular dysfunction (LVD) secondary to coronary artery disease (CAD) patients. OBJECTIVE: We sought to determine the role of MYBPC3 25 bp polymorphism on LVD in two cohorts of CAD patients. METHODS AND RESULTS: The study included 265 consecutive patients with angiographically confirmed CAD and 220 controls. MYBPC3 25 bp polymorphism was determined by polymerase chain reaction. Our results showed that carrier status of MYBPC3 25 bp deletion was associated with significant compromised left ventricle ejection fraction (LVEF ≤45) in CAD patients (p value  =  <0.001; OR = 4.49). To validate our results, we performed a replication study in additional 140 cases with similar clinical characteristics and results again confirmed consistent findings (p = 0.029; OR = 3.3). Also, presence of the gene deletion did not have significant association in CAD patients with preserved ejection fraction (LVEF>45) (p value  = 0.1; OR  = 2.3). CONCLUSION: The frequency of MYBPC3 DW genotype and D allele was associated with compromised LVEF implying that genetic variants of MYBPC3 encoding mutant structural sarcomere protein could increase susceptibility to left ventricular dysfunction. Therefore, 25 bp deletion in MYBPC3 may represent a genetic marker for cardiac failure in CAD patients from Southeast Asia.

Identification and characterization of novel small-molecule inhibitors against hepatitis delta virus replication by using docking strategies.

BACKGROUND: The small delta antigen protein of hepatitis delta virus (HDV) has been shown to be important for replication of the virus and essential for the viral life cycle. Therefore, it may be an appropriate target for designing biological experiments for drug development to identify the potential inhibitors of hepatitis D. OBJECTIVES: To identify a novel molecule as possible drug candidate for the treatment of Hepatitis D. MATERIALS AND METHODS: In the present study, a computational approach was used for the identification of novel small-molecule inhibitors against HDV replication using docking studies. An Autodock tool was used for docking and identifying the active binding sites in target proteins. The Lipinski filter and preADMET program were also used for determining the pharmacokinetic properties in order to filter out potential ligand molecules to restrain virus replication. RESULTS: Our results suggest that pyridinone (3-[(4,7-dichloro-1,3-benzoxazol-2-yl) methylamino]-5-ethyl-6-methyl-pyridin-2(1H)-one) is a validated potential inhibitor of HDV replication and could be as a novel antiviral drug for the treatment of hepatitis D. COUNCLUSIONS: We have identified a novel antiviral drug by using innovative computational approaches. The results provide a basis to experimentally develop into drug which can be used for the treatment of delta hepatitis.

Predicted RNA secondary structures for the conserved regions in dengue virus.

Dengue fever, dengue hemorrhagic fever and dengue shock syndrome are the prevalent mosquito borne viral infections worldwide. The dengue virus belongs to the genus flavivirus with conserved RNA domains peptidase_S7 and dexHc among its members. The secondary structures for RNA domains peptidase_S7 and DexHc are hence predicted and discussed with other known viral RNA structures to glean structural insights through comparison.

A database for anti-diabetic plants with clinical / experimental trials.

UNLABELLED: A number of plants have been described in Ayurveda and other traditional medicine for the management of diabetes. However, information about them is not easily available. Active constituents of any medicinal plant define the efficacy and safety of treatment to control hyperglycemia. We describe the database to maintain the record of medicinal plants having anti-hyperglycemic or anti-diabetic activity. The database contains information such as plant name, its geographical distribution, useful plant part, known dosage, active constituents, mechanism of action and clinical/experimental data. The database also includes information about plant raw material suppliers or manufacturers in India. The current database includes 238 plants species and 123 Indian industries using them. AVAILABILITY: The database is freely available at http://www.biotechpark.org.in/antidia/index.html.

Identification and analysis of putative promoter motifs in Flavivirus genome.

The genus Flavivirus comprises medically significant pathogenic virus; causing several infections in humans worldwide. Flavivirus genomes are 10-11 kb approximately and encode both structural and non structural region. The non structural region plays fundamental role in the stability, regulation and cell cycle of virus. The complete genomes of 26 Flavivirus were used for identification of promoter motifs through in silico approaches. The promoter sequences were encoded in merely 16 viruses and 10 viruses could not encode it. All these in silico identified promoter motifs was confirmed and verified with the known experimental data. This analysis suggests that presence of promoter may play a crucial role in the pattern of gene expression, regulation networks, cell specificity and development. It may also be useful for designing efficient expression vector and target specific delivery system in the gene therapy.

DNA damage and mutagenicity induced by endosulfan and its metabolites.

Endosulfan is a widely used broad-spectrum organochlorine pesticide, which acts as a contact and stomach poison. Nontarget species, such as cattle, fish, birds, and even humans, are also affected. Studies on the genotoxicity and mutagenicity of endosulfan have been inconsistent and nothing is known about the genotoxicity of its metabolites. In the present study, endosulfan (as a commercial isomeric mixture and as the alpha- and beta-isomers), and metabolites of endosulfan (the sulfate, lactone, ether, hydroxyether, and diol derivatives) were assayed for their ability to induce DNA damage in Chinese hamster ovary (CHO) cells and human lymphocytes using the Comet assay and were assayed for their mutagenicity using the Salmonella reversion assay (Ames test with TA98, TA97a, TA102, TA104, and TA100, with and without S9 activation). The compounds produced statistically significant (P < 0.01), concentration-dependent (0.25-10 microM) increases in DNA damage in both CHO cells and human lymphocytes. Endosulfan lactone caused the most DNA damage in CHO cells, while the isomeric mixture of endosulfan produced the greatest response in lymphocytes. The test compounds also were mutagenic in Salmonella strains at concentrations of 1-20 mug/plate (P < 0.05), with TA98 being the most sensitive strain and the diol and hydroxyether metabolites producing the highest responses. The results indicate that exposure to sublethal doses of endosulfan and its metabolites induces DNA damage and mutation. The contribution of the metabolites to the genotoxicity of the parent compound in Salmonella and mammalian cells, however, is unclear, and the pathways leading to bacterial mutation and mammalian cell DNA damage appear to differ.

Effect of lead exposure on the immune response of some occupationally exposed individuals.

Lead is a ubiquitous pollutant in the industrial environment, which poses serious threats to human health. In the past 20 years increasing attention has been paid to the effects of lead exposure on health. This toxic metal alters the immune response of animals as well as humans. To study the immunological effects of occupational exposure to lead, we examined lymphocyte proliferation, natural killer (NK) cell cytotoxicity and interferon-gamma production with peripheral blood mononuclear cells (PBMCs) of individuals occupationally exposed to lead. We selected three different groups of individuals exposed to lead: three-wheeler drivers (30), battery workers (34) and silver jewelery makers (20); and unexposed healthy volunteers (30) as control for comparison. Our results indicate that though lymphocyte proliferation to phytohaemagglutinin (PHA) is inhibited in lead exposed individuals as compared with unexposed volunteers, there is no correlation between inhibition of lymphocyte proliferation and blood lead level. NK cell cytotoxicity remains unaffected in individuals exposed to lead as compared with controls. On the other hand, we observed that interferon-gamma (IFN-gamma) was significantly elevated in T cell mitogen, PHA, stimulated PBMCs culture supernatant of lead exposed individuals. We found significant positive correlation between blood lead levels and IFN-gamma produced in culture supernatant on stimulation with PHA. In brief, this study demonstrates that lead can affect the immune response of the occupationally exposed individuals such as three-wheeler drivers, battery reconditioning workers and silver jewelery makers.

Methanol-induced neurotoxicity in pups exposed during lactation through mother: role of folic acid.

Role of folic acid on methanol-induced neurotoxicity was studied in pups at Postnatal Day (PND) 45 exposed to methanol (1%, 2% and 4%, v/v) during lactation through mothers maintained on folic acid-deficient (FD) and folic acid-sufficient (FS) diet. A gradual loss in the body weight gain was observed in the pups exposed to 2% and 4% methanol in the FD group, while FS group exhibited this alteration only at 4% exposure. The assessment of spontaneous locomotor activity (SLA) showing a significant increase in the distance travelled was observed in the 2% and 4% methanol-exposed groups in both the FS and FD animals when compared with their respective controls, but the effect was more marked in the FD group. A significant decrease in the conditioned avoidance response (CAR) was observed in pups exposed to 2% and 4% methanol in the FD group at PND 45. The results also suggest that disturbances in dopaminergic and cholinergic receptors were more pronounced in the FD group as compared to the FS group. A significant decrease in striatal dopamine levels was also observed in the FD group at 2% and 4% methanol exposure, while in the FS group, a significant decrease was exhibited only at 4% methanol exposure. An aberrant increase in the expression of Growth-Associated Protein (GAP-43), a neuron-specific growth-associated protein was observed in pups in the FD group exposed to 2% and 4% methanol, while an increase in the expression of GAP-43 in the FS group was found only at 4% methanol exposure in the hippocampal region as compared to their respective controls. Results suggests that methanol exposure during growth spurt period adversely affects the developing brain, the effect being more pronounced in FD rats as compared to FS rats, suggesting a possible role of folic acid in methanol-induced neurotoxicity.