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Density functional theory (DFT) was performed in the gas phase to investigate the tautomerization and transitions in efavirenz. The amide and imidic tautomers' geometrical parameters are performed using B3LYP/6-31++G** and M06-2X/ cc-pVTZ (-F). The results showed that the amide tautomer is more stable than the imidic tautomer in the gas phase. The non-linear optical (NLO) properties of the amide and imidic tautomers are computed. Interestingly, the amide and imidic forms may be an attractive compound in enhancing NLO constituents due to their valuable non-linear property. Natural bond orbital (NBO) analyses have been performed on the amide and imidic tautomers. The substantial differences in occupancies and the energies of bonding and anti-bonding orbital have been analyzed and described. Notably, thermodynamic (Gibbs free energy, entropy, and enthalpy) properties of proton intra-migration of the tautomers via a single proton shift in the gas phase were predicted. The detailed results revealed that the kinetic and thermodynamic favorability increased from imidic tautomer to amide, hence the pathway to the amide arrangement of efavirenz is a favorable reaction. Besides this, the electrostatic potential surface plots have been used to explore the possible site for electron-withdrawing and donating. The frontier molecular orbital reveals the energy gap and chemical activity of the tautomers.
Maryam Amra Jordaan; Oluwakemi Ebenezer; Khethiwe Mthiyane; Nkululeko Damoyi; Michael Shapi. Amide imidic prototropic tautomerization of efavirenz, NBO analysis, hyperpolarizability, polarizability and HOMO–LUMO calculations using density functional theory. Computational and Theoretical Chemistry 2021, 1201, 113273 .
AMA StyleMaryam Amra Jordaan, Oluwakemi Ebenezer, Khethiwe Mthiyane, Nkululeko Damoyi, Michael Shapi. Amide imidic prototropic tautomerization of efavirenz, NBO analysis, hyperpolarizability, polarizability and HOMO–LUMO calculations using density functional theory. Computational and Theoretical Chemistry. 2021; 1201 ():113273.
Chicago/Turabian StyleMaryam Amra Jordaan; Oluwakemi Ebenezer; Khethiwe Mthiyane; Nkululeko Damoyi; Michael Shapi. 2021. "Amide imidic prototropic tautomerization of efavirenz, NBO analysis, hyperpolarizability, polarizability and HOMO–LUMO calculations using density functional theory." Computational and Theoretical Chemistry 1201, no. : 113273.
Noroviruses are non-enveloped viruses with a positive-sense single-stranded RNA (ssRNA) genome belonging to the genus Norovirus, from the family Caliciviridae, which are accountable for acute gastroenteritis in humans. The Norovirus genus is subdivided into seven genogroups, i.e., (GI-GVII); among these, the genogroup II and genotype 4 (GII.4) strains caused global outbreaks of human norovirus (HuNov) disease. The viral genome comprises three open reading frames (ORFs). ORF1 encodes the nonstructural polyprotein that is cleaved into six nonstructural proteins, which include 3C-like cysteine protease (3CLpro) and a viral RNA-dependent RNA polymerase. ORF2 and ORF3 encode the proteins VP1 and VP2. The RNA-dependent RNA polymerase (RdRp) from noroviruses is one of the multipurpose enzymes of RNA viruses vital for replicating and transcribing the viral genome, making the virally encoded enzyme one of the critical targets for the development of novel anti-norovirus agents. In the quest for a new antiviral agent that could combat HuNov, high throughput virtual screening (HTVS), combined with e-pharmacophore screening, was applied to screen compounds from the PubChem database. CMX521 molecule was selected as a prototype for a similarity search in the PubChem online database. Molecular dynamics simulations were employed to identify different compounds that may inhibit HuNov. The results predicted that compound CID-57930781 and CID-44396095 formed stable complexes with MNV-RdRp within 50 ns; hence, they may signify as promising human norovirus inhibitors.
Oluwakemi Ebenezer; Maryam A. Jordaan; Nkululeko Damoyi; Michael Shapi. Discovery of Potential Inhibitors for RNA-Dependent RNA Polymerase of Norovirus: Virtual Screening, and Molecular Dynamics. International Journal of Molecular Sciences 2020, 22, 171 .
AMA StyleOluwakemi Ebenezer, Maryam A. Jordaan, Nkululeko Damoyi, Michael Shapi. Discovery of Potential Inhibitors for RNA-Dependent RNA Polymerase of Norovirus: Virtual Screening, and Molecular Dynamics. International Journal of Molecular Sciences. 2020; 22 (1):171.
Chicago/Turabian StyleOluwakemi Ebenezer; Maryam A. Jordaan; Nkululeko Damoyi; Michael Shapi. 2020. "Discovery of Potential Inhibitors for RNA-Dependent RNA Polymerase of Norovirus: Virtual Screening, and Molecular Dynamics." International Journal of Molecular Sciences 22, no. 1: 171.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed as the causative virus of COVID-19 disease, which is currently a worldwide pandemic. Efavirenz, a non-nucleoside reverse transcriptase inhibitor (NNRTI), is one of the most potent chemical compounds proposed to treat COVID-19 infection. We, therefore, performed virtual screening on FDA approved drugs that are similar to the efavirenz moiety. Subsequently, the compounds were subjected to screening by analyzing their drug-likeness, such as Lipinski's rule of five and ADMET properties. Molecular docking study revealed that Met165, His41, His163, and Phe140 were important interacting residues for COVID-19 main protease receptor-ligand interaction. Five top-ranked compounds, podophyllotoxin, oxacillin, lovastatin, simvastatin, and gefitinib, were selected by virtual screening and docking studies. The highest occupied molecular (HOMO) orbital, lowest unoccupied molecular orbital (LUMO) and energy gap values was calculated using density functional theory (DFT). The results of the study showed that lovastatin and simvastatin might be considered as lead compounds for further development for COVID-19 main protease inhibitors.
Maryam A. Jordaan; Oluwakemi Ebenezer; Nkululeko Damoyi; Michael Shapi. Virtual screening, molecular docking studies and DFT calculations of FDA approved compounds similar to the non-nucleoside reverse transcriptase inhibitor (NNRTI) efavirenz. Heliyon 2020, 6, e04642 -e04642.
AMA StyleMaryam A. Jordaan, Oluwakemi Ebenezer, Nkululeko Damoyi, Michael Shapi. Virtual screening, molecular docking studies and DFT calculations of FDA approved compounds similar to the non-nucleoside reverse transcriptase inhibitor (NNRTI) efavirenz. Heliyon. 2020; 6 (8):e04642-e04642.
Chicago/Turabian StyleMaryam A. Jordaan; Oluwakemi Ebenezer; Nkululeko Damoyi; Michael Shapi. 2020. "Virtual screening, molecular docking studies and DFT calculations of FDA approved compounds similar to the non-nucleoside reverse transcriptase inhibitor (NNRTI) efavirenz." Heliyon 6, no. 8: e04642-e04642.
Due to the migratory flow of infected people with severe acute respiratory syndrome virus (SARS-CoV-2), the numbers of confirmed cases of coronavirus 2019 (COVID-19) infections is accelerating worldwide and pre-clinical evidence of antiviral agents that can combat this pandemic is still elusive. We identified published SAR-CoV efficacy experiments in which some selected compounds were used to test the reduction of the virus load in mice. We then developed a combined model based on scoping review, meta-analyses, and molecular docking studies to evaluate the effect size of preclinical studies of compounds that have been tested against SARS-CoV. Molecular docking studies of the inhibitors in the active pocket of COVID-19 protease were also performed. Our results identified three SARS-CoV inhibitors i.e. EIDD-2801, GS-5734 and amodiaquine that are excellent options for optimization and drug development to treat or cure COVID-19.
Oluwakemi Ebenezer; Maryam Amra Jordaan; Nkululeko Damoyi; Ropo Ogunsakin; Michael Shapi. Identification of SARS-CoV-2 preclinical (in vivo) compounds targeting COVID-19 main protease: A scoping review, meta-analysis and molecular docking studies. 2020, 1 .
AMA StyleOluwakemi Ebenezer, Maryam Amra Jordaan, Nkululeko Damoyi, Ropo Ogunsakin, Michael Shapi. Identification of SARS-CoV-2 preclinical (in vivo) compounds targeting COVID-19 main protease: A scoping review, meta-analysis and molecular docking studies. . 2020; ():1.
Chicago/Turabian StyleOluwakemi Ebenezer; Maryam Amra Jordaan; Nkululeko Damoyi; Ropo Ogunsakin; Michael Shapi. 2020. "Identification of SARS-CoV-2 preclinical (in vivo) compounds targeting COVID-19 main protease: A scoping review, meta-analysis and molecular docking studies." , no. : 1.
The Mintails Mogale Gold (MMG) and the Rand Uranium (RU) are two large-scale mining consortiums active in re-mining old tailings dams and dumps in Krugersdorp and are a source of mine discharge feed into the Krugersdorp Game Reserve (KGR). This has resulted in a noticeable accumulation of potentially harmful elements (PHEs) over a number of years. Efforts were implemented to interpret the concentration levels of PHEs in soils of the study areas of which a total of 36 georeferenced soil samples were collected (in triplicate) from the MMG, RU and KGR, including samples from farmlands and waterways adjacent to the mining sites. Samples were then analysed by both inductively coupled plasma optical emission spectrometry (ICP-OES) and inductively coupled plasma mass spectrometry (ICP-MS) for 36 elements. From the 36 elements of this study, detailed evaluations of the occurrence of 12 selected elements were discussed. The geochemical landscape at the KGR is shown to be in flux. The major mediating influences on the behaviour of As, Co, Cu, Hg and Pb, as they enter the KGR largely in the form of acid mine drainage (AMD), are the geological substrate (mostly in carbonate form). Analysis of the soils showed high levels of contamination for As and Co in ppm. The mean maximum of As ranged from (5.00–170.30) with the highest level found in the Krugersdorp site. The mean maximum of Co ranged from (46.00–102.30) with the highest level found in MMG. All of these values were well above the recommended maximum acceptable concentration (MAC) values, i.e., As (15–20) and Co (20–50). The mean maximum values for Pb (12.40–92.30); Cu (18.50–115.30) and Hg (12.40–92.30) content in surface soils of all four segments studied falls well within the MAC range for agricultural soils i.e., Cu (60–150); Hg (0.5–5) and Pb (20–300).
Michael Shapi; Maryam Amra Jordaan; Devandren Subramoney Nadasan; Theophilus C. Davies; Emmanuel Chirenje; Mpumelelo Dube; Mammusa R. Lekoa. Analysis of the Distribution of Some Potentially Harmful Elements (PHEs) in the Krugersdorp Game Reserve, Gauteng, South Africa. Minerals 2020, 10, 151 .
AMA StyleMichael Shapi, Maryam Amra Jordaan, Devandren Subramoney Nadasan, Theophilus C. Davies, Emmanuel Chirenje, Mpumelelo Dube, Mammusa R. Lekoa. Analysis of the Distribution of Some Potentially Harmful Elements (PHEs) in the Krugersdorp Game Reserve, Gauteng, South Africa. Minerals. 2020; 10 (2):151.
Chicago/Turabian StyleMichael Shapi; Maryam Amra Jordaan; Devandren Subramoney Nadasan; Theophilus C. Davies; Emmanuel Chirenje; Mpumelelo Dube; Mammusa R. Lekoa. 2020. "Analysis of the Distribution of Some Potentially Harmful Elements (PHEs) in the Krugersdorp Game Reserve, Gauteng, South Africa." Minerals 10, no. 2: 151.
This study was designed to determine the extent to which alluvial and bedrock gold mining activities in the Kette-Batouri region of Eastern Cameroon are responsible for the discharge of potentially harmful elements (PHEs) into natural water bodies. This is considered to be of great public concern, since elevated levels of PHEs in these water bodies, which are widely used for domestic purposes, could have adverse health and environmental effects on the population and nearby ecosystems. The investigation into the levels of PHEs in natural water bodies of this area was conducted to ascertain the toxicity posed by mine waste stockpiles as data from the literature on this subject are scarce. Forty-two water samples from the region were analysed for some 60 PHEs by ICP-OES, of which 22 that were not below the detection limit were considered for further data analysis. Maximum total concentrations in water of As, Cr, Pb, and V and Zn are above the World Health Organization (WHO) maximum allowable concentration (MAC) levels and are as follows (μg l−1): As (21.90–50.9); Cr (1.80–57.30); Pb (0.50–34.70); V (24.70–77.20) and Zn (3.10–481.70). This information is consistent with that of our recent research efforts which have indicated moderate pollution by heavy metals in the soils with a slight deterioration of site quality in this region. The data generated from this investigation is important in the formulation of water management strategies and recommendations for remediation of water bodies at abandoned mine sites for meeting water quality standards.
M. A. Jordaan; M. E. Mimba; S. C. NguemheFils; B. T. Edith-Etakah; M. Shapi; J. Penaye; T. C. Davies. Occurrence and levels of potentially harmful elements (PHEs) in natural waters of the gold mining areas of the Kette-Batouri region of Eastern Cameroon. Environmental Monitoring and Assessment 2018, 190, 416 .
AMA StyleM. A. Jordaan, M. E. Mimba, S. C. NguemheFils, B. T. Edith-Etakah, M. Shapi, J. Penaye, T. C. Davies. Occurrence and levels of potentially harmful elements (PHEs) in natural waters of the gold mining areas of the Kette-Batouri region of Eastern Cameroon. Environmental Monitoring and Assessment. 2018; 190 (7):416.
Chicago/Turabian StyleM. A. Jordaan; M. E. Mimba; S. C. NguemheFils; B. T. Edith-Etakah; M. Shapi; J. Penaye; T. C. Davies. 2018. "Occurrence and levels of potentially harmful elements (PHEs) in natural waters of the gold mining areas of the Kette-Batouri region of Eastern Cameroon." Environmental Monitoring and Assessment 190, no. 7: 416.
Background: Alluvial and bedrock gold mining as well as ore processing are predominant activities prevalent in the Kette-Batouri Region. These activities cause soil pollution by way of the accumulation and distribution of toxic, potentially harmful elements (PHEs). For the first time, the migration patterns and toxicity potential of PHEs in the soil of the gold mining district of the Kette-Batouri region is demonstrated. The data were sought as background information necessary for the design of suitable pollution monitoring schemes along with the development of guidelines for performing such monitoring. Materials and Methods: A total of 30 surface soil samples were collected and analysed for a selected number of PHEs by Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES). Results: Concentration ranges obtained (mg kg–1) for total PHE were: Cu (4-15), Zn (5-18), Ni (3-17), Co (0.5-10), Mn (40-564), V (31-263), Cr (13-123), Fe (9000-127300) As (1-9), Pb (1.5-26) and Cd (0.25). Statistical analyses showed that the mean concentrations were mostly lower than reference background values. The highest in PHE concentrations were obtained only for Cr and V, at sectors of farmlands that are directly adjacent to the mining localities. Basic and multivariate statistical analyses (principal component analysis/varimax rotated component analysis) were performed to reduce the multi-dimensional space of variables and samples, thus defining two distinct sets of PHE associations as tracers of natural and anthropogenic influences. These associations, viz., (Cu-Pb-Ni-As-Cr-Fe-V) and (Zn-Co-Mn), accounted for 76.93% of the total variance. Conclusion: Geoaccumulation indices show that the soils in Kette-Batouri are unpolluted to moderately polluted. However, calculated Pollution Load Indices (PLI) indicated a slight deterioration of site quality, which requires further investigation. The effectiveness of the accrued dataset for monitoring PHEs pollution in the area and for strengthening other aspects of future ecological risk assessment campaigns is demonstrated.
M.A. Jordaan; B.T. Edith-Etakah; M. Shapi; J. Penaye; M.E. Mimba; S.C. NguemheFils; D.S. Nadasan; T.C. Davies. Background Concentrations of Potentially Harmful Elements in Soils of the Kette-Batouri Region, Eastern Cameroon. Research Journal of Environmental Toxicology 2016, 11, 40 -54.
AMA StyleM.A. Jordaan, B.T. Edith-Etakah, M. Shapi, J. Penaye, M.E. Mimba, S.C. NguemheFils, D.S. Nadasan, T.C. Davies. Background Concentrations of Potentially Harmful Elements in Soils of the Kette-Batouri Region, Eastern Cameroon. Research Journal of Environmental Toxicology. 2016; 11 (1):40-54.
Chicago/Turabian StyleM.A. Jordaan; B.T. Edith-Etakah; M. Shapi; J. Penaye; M.E. Mimba; S.C. NguemheFils; D.S. Nadasan; T.C. Davies. 2016. "Background Concentrations of Potentially Harmful Elements in Soils of the Kette-Batouri Region, Eastern Cameroon." Research Journal of Environmental Toxicology 11, no. 1: 40-54.
O Ebenezer; Ma Jordaan; Re Ogunsakin; M Shapi. Potential SARS-COV preclinical (in vivo) compounds targeting COVID-19 main protease: a meta-analysis and molecular docking studies. 2021, 24, 99 -106.
AMA StyleO Ebenezer, Ma Jordaan, Re Ogunsakin, M Shapi. Potential SARS-COV preclinical (in vivo) compounds targeting COVID-19 main protease: a meta-analysis and molecular docking studies. . 2021; 24 (3):99-106.
Chicago/Turabian StyleO Ebenezer; Ma Jordaan; Re Ogunsakin; M Shapi. 2021. "Potential SARS-COV preclinical (in vivo) compounds targeting COVID-19 main protease: a meta-analysis and molecular docking studies." 24, no. 3: 99-106.