The novel coronavirus of 2019 (nCoV-19) has become a pandemic, affecting over 205 nations with over 7,410,000 confirmed cases which has resulted to over 418,000 deaths worldwide. This study aimed to identify potential therapeutic compounds and phytochemicals of medicinal plants that have potential to modulate the expression network of genes that are involve in SARS-CoV-2 pathology in human host and to understand the dynamics key proteins involved in the virus-host interactions. The method used include gene network analysis, molecular docking, and sequence and structure dynamics simulations. The results identified DNA-dependent protein kinase (DNA-PK) and Protein kinase CK2 as key players in SARS-CoV-2 lifecycle. Among the predicted drugs compounds, clemizole, monorden, spironolactone and tanespimycin showed high binding energies; among the studied repurposing compounds, remdesivir, simeprevir and valinomycin showed high binding energies; among the predicted acidic compounds, acetylursolic acid and hardwickiic acid gave high binding energies; while among the studied anthraquinones and glycosides compounds, ellagitannin and friedelanone showed high binding energies against 3-Chymotrypsin-like protease (3CL pro), Papain-like protease (PL pro), helicase (nsp13), RNA-dependent RNA polymerase (nsp12), 2'-O-ribose methyltransferase (nsp16) of SARS-CoV-2 and DNA-PK and CK2alpha in human. The order of affinity for CoV proteins is 5Y3E > 6NUS > 6JYT > 2XYR > 3VB6. Finally, medicinal plants with phytochemicals such as caffeine, ellagic acid, quercetin and their derivatives could possibly remediate COVID-19.

Diarrhoeal disease kills about 1.5 million human beings per year across the continents. The enterotoxigenic Escherichia coli (ETEC) pathotype has been noted as a major cause of diarrheal disease in human and livestock. The aim of this study is to identify broad-spectrum molecular targets in bacteria and broad-spectrum lead compounds (functional inhibitors) with high efficacy and no significant adverse implication on human systems, in relevance to diarrhea therapy through computational approaches which include phylogenetics, target prediction, molecular docking, and molecular flexibility dynamic simulations. Three molecular target genes, murA, dxr, and DnaE, which code for uridine diphosphate-N-acetylglucosamine-1-carboxyvinyltransferase, 1-deoxy-D-xylulose-5-phosphate reductoisomerase, and deoxyribonucleic acid polymerase III alpha subunit, respectively, were found to be highly conserved in 7 diarrhea-causing microbes. In addition, 21 potential compounds identified showed varied degree of affinity to these enzymes. At free energy cutoff of −8.0 kcal/mol, the highest effective molecular target was DNA polymerase III alpha subunit (PDB ID: 4JOM) followed by UDP-N-acetylglucosamine-1-carboxyvinyltransferase (PDB ID: 5UJS), and 1-deoxy-D-xylulose-5-phosphate reductoisomerase (PDB ID: 1ONN), while the highest effective lead compound was N-coeleneterazine followed by amphotericin B, MMV010576, MMV687800, MMV028694, azithromycin, and diphenoxylate. The flexibility dynamics of DNA polymerase III alpha subunit unraveled the atomic fluctuation which potentially implicated Asp593 as unstable active site amino acid residue. In conclusion, bacteria DnaE gene or its protein is a highly promising molecular target for the next generation of antibacterial drugs of the class of N-coeleneterazine.

The soil is a key component of natural ecosystems because environmental sustainability depends largely on a sustainable soil ecosystem. The objective of this study was to predict the impact of selected toxic compounds from dumpsite or contaminated soils on human health at the molecular level of biological processes. The in silico methods that were used include toxicokinetics and target gene prediction, molecular docking, and gene expressing network analysis. The result showed bisphenol A (BPA), 2,20-bis(p-chlorophenyl)-1,1-dichloroethane (DDD), 2,20-bis(p-chlorophenyl)-1,1-trichloroethane (DDT), diethylhexyl phthalate (DEHP), nonylphenol (NP) and tetrachlorodibenzodioxin (TCDD) as the active toxic compounds that can modulate biological system and are considered as potential cause of several diseases including cancer. The principal target genes include substance-P receptor (also known as Neurokinin 1 receptor), 5-hydroxytryptamine receptor, human serotonin transporter; estrogen receptor alpha; and aryl hydrocarbon receptor. These genes implicated SUZ12, STAT3, and TRIM28 as the major transcription factors while mitogen-activated protein kinases and cyclin-dependent kinases were the major kinases from the protein-protein interaction. All the six toxicants investigated showed good free binding energies (ΔG) which were below - 5.0 kcal.mol−1. These toxic compounds showed ligand efficiency greater than 0.25 kcal.mol−1. HA and would possibly cause fatal damage on human health. The order of in silico predicted toxicity of these compounds were BPA > DDD = DDT > TCDD > NP > DEHP. Our results identified potential threats, which the selected toxicants can pose to public health. More importantly, it provides basis for investigation of super bugs (microorganisms) that can remediate these toxicants in our environment. Environmental monitoring and modern wastes management system should be implemented and enforced in the affected countries in order to safeguard the health of the citizenry.

Melanin is s most widely distributed pigment and is found in bacteria, fungi, plants, and animals. Melanogenesis is under complex regulatory control by multiple agents interacting through pathways activated by hormonal and receptor-dependent and -independent mechanisms. There are about 20 genes that are involved in the biochemical pathway of melanogenesis and its regulation, which include: tyrosinase, microphthalmia-associated transcription factor, melanocortin1 receptor, adenylate cyclase, protein kinase A. Human melanogenesis regulatory proteins such as MAPK1, CREB3, and CREBP, have binary interaction with the protein of herpesvirus, hepatitis C virus, Human immunodeficiency virus type 1, Simian virus 40, and Human adenovirus A and C. Melanin is a double-edged sword in host-pathogen interaction (e.g., human-bacteria and/or fungi interaction). The inducers of upregulation of melanogenesis include fluvoxamine, famotidine, terbutaline, heliotrine, sirolimus, dicoumarol, Prestwick-860, carbimazole, (-)-MK-801, rilmenidine, hydrastine hydrochloride, haloperidol, scopolamine N-oxide, raubasine, and dihydroergocristine. In melanogenesis, GSK3B, CSNK2A, MAPK1, MAPK3, MAPK14, ERK1, and HIPK2 were the major kinases, while RUNX1, GATA1, and REST, SUN12, and RCOR1 were the major transcription factors. This study has reviewed the melanogenesis pathway, its regulations as well as applications to viral infection. The antiviral activity of melanin and its complex in the presence of antibacterial and antifungal compounds should be investigated to further provide insight for biomedical, biotechnological, and pharmacological applications.

This study aimed to determine the molecular identities and genetic relatedness of rhizobia isolated from pigeon pea and pinto beans, and assess their remediation potential in the presence of 1 %, 3 % and 5 % (w/v) crude oil in minimal medium for 7 days incubation period. Standard microbiological and molecular methods which include amplification and purification of 16S rRNA, agarose gel electrophoresis, and sequencing. Results showed molecular identities of six rhizobia from pigeon peas as Bradyrhizobium diazoefficiens USDA122, Rhizobium leguminosarum WSM2304, Bradyrhizobium japonicum N61, Rhizobium leguminosarum N741, Rhizobium leguminosarum BIHIB1217, and Bradyrhizobium japonicum E109; and three rhizobia obtained from pinto beans were Rhizobium leguminosarum N871, Bradyrhizobium diazoefficiens USDA110 and Bradyrhizobium japonicum SEMIA5079. All tested rhizobia (9) showed petroleum degradation ability, as they all grew in the 1, 3 and 5 % (w/v) crude oil minimal medium under laboratory conditions. B. diazoefficiens USDA122 showed the highest optical density (OD) value of 1.184 ± 0.05 on 7th day at 1 % (w/v) crude oil contamination, while R. leguminosarum N741 has the lowest OD value of 0.372 ± 0.02 at 5 % (w/v) crude oil on 7th day. For all the rhizobia, increase occurred throughout incubation period at 1, 3 and 5 % (w/v) except Rhizobium leguminosarum N741 and R. leguminosarum BIHIB1217. In conclusion, the association of R. leguminosarum BIHIB1217 and R. leguminosarum N871 from pigeon pea and pinto beans respectively, were found most effective in crude oil degradation and thus they are recommended as a promising association for remediation of crude oil spilled soils.