UDOM IR :: Browsing by Author "Vuai, Said A. H."

Browsing by Author "Vuai, Said A. H."

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Abrogating the nsp10–nsp16 switching mechanisms in SARS-CoV-2 by phytochemicals from Withania somnifera: a molecular dynamics study
(Taylor & Francis, 2021) Vuai, Said A. H.; Onokaa, Isaac; Sahini, Mtabazi G.; Swai, Hulda S.; Shadrack, Daniel M.
The search for therapeutic small molecules and vaccines for Covid-19 treatment is an urgent but evolving topic. The virus has claimed over 3,782,490 lives (as of 12 June 2021), with the figure expected to rise due to the high versatility of the SAR-CoV-2 variant. Therapeutic options based on SARS-CoV-2 inhibitor are essential. Withanolides have a long history in traditional medicines with versatile biological properties including antiviral activities. In this study, the inhibitory potential of withanolides from Withania somnifera (Ashwagandha) against SARS-CoV-2 non-structural protein 10 (nsp10) was investigated by employing atomistic in silico methods viz molecular docking, molecular dynamics and binding free energy calculations. Investigated Withania somnifera compounds demonstrated binding affinity to the nsp10 and in its complex form, that is, nsp10-nsp16 heterodimer. Two withanolides; withanoside IV and withanoside V isolated from the roots of Withania somnifera demonstrated strong inhibition with binding free energies of −29.5 and −29.1 kJ/mol, respectively. Molecular dynamics and binding free energy ascertained the stability of withanoside IV. Water molecules, although known to play an important role in mediating biological systems, herein, water was found to have a repulsive binding effect to some residues, suggesting that the binding of withanoside IV would require dewetting of the nsp10 or displacing the water to bulk solvents. Interestingly, residues in the nsp10 that are responsible for forming stable interaction at the nsp10–nsp16 were found to be strongly interacting with withanoside IV, hence weakening the nsp10–nsp16 interaction and recognition. Further in vitro and in vivo experiments are recommended to validate the anti-SARS-COV-2 potential of these phytochemicals.
Abrogating the nsp10–nsp16 switching mechanisms in SARS-CoV-2 by phytochemicals from Withania somnifera: a molecular dynamics study
(Taylor & Francis, 2021) Vuai, Said A. H.; Onoka, Isaac; Sahini, Mtabazi G.; Swai, Hulda S.; Shadrack, Daniel M.
The search for therapeutic small molecules and vaccines for Covid-19 treatment is an urgent but evolving topic. The virus has claimed over 3,782,490 lives (as of 12 June 2021), with the figure expected to rise due to the high versatility of the SAR-CoV-2 variant. Therapeutic options based on SARS-CoV-2 inhibitor are essential. Withanolides have a long history in traditional medicines with versatile biological properties including antiviral activities. In this study, the inhibitory potential of withanolides from Withania somnifera (Ashwagandha) against SARS-CoV-2 non-structural protein 10 (nsp10) was investigated by employing atomistic in silico methods viz molecular docking, molecular dynamics and binding free energy calculations. Investigated Withania somnifera compounds demonstrated binding affinity to the nsp10 and in its complex form, that is, nsp10-nsp16 heterodimer. Two withanolides; withanoside IV and withanoside V isolated from the roots of Withania somnifera demonstrated strong inhibition with binding free energies of −29.5 and −29.1 kJ/mol, respectively. Molecular dynamics and binding free energy ascertained the stability of withanoside IV. Water molecules, although known to play an important role in mediating biological systems, herein, water was found to have a repulsive binding effect to some residues, suggesting that the binding of withanoside IV would require dewetting of the nsp10 or displacing the water to bulk solvents. Interestingly, residues in the nsp10 that are responsible for forming stable interaction at the nsp10–nsp16 were found to be strongly interacting with withanoside IV, hence weakening the nsp10–nsp16 interaction and recognition. Further in vitro and in vivo experiments are recommended to validate the anti-SARS-COV-2 potential of these phytochemicals.
Cation–π interactions drive hydrophobic self-assembly and aggregation of niclosamide in water †
(The Royal Society of Chemistry, 2021) Vuai, Said A. H.; Sahini, Mtabazi G.; Onoka, Isaac; Kiruri, Lucy W.; Shadrack, Daniel M.
The beneficial medicinal effects of niclosamide have been reported to be hampered by poor aqueous solubility and so a higher concentration dosage is required. In this work, we have studied the aggregation properties of niclosamide in water by varying the number of monomers. We have employed all-atom classical molecular dynamics simulation in order to explore such properties. The equilibrium structure exists in an aggregated state with structural rearrangements of the stacking units. Niclosamide monomers tend to form clusters in an orderly manner and tend to aggregate in parallel and antiparallel orientations of the phenyl rings as the monomers are increased in number from 4 to 9. Upon increasing the size from 9 to 14, and from 49 to 150, a considerable dominance of the metastable parallel arrangement is observed, resulting in the formation of a closely packed cluster with hydrophobic contacts. The metastable conformation self-arranges to a T-shape before forming a stable planar antiparallel displaced conformation. The aggregated π–π parallel and cation–π antiparallel clusters in water exist in a β-conformer. We further observed that formation of a stable cluster aggregate entails the formation of an intermediate metastable cluster that disperses in solution forming a large stable cluster. We also discovered that movement of the water is faster in less aggregated clusters and as the cluster size increases, the mobility rate becomes much slower.
Characterization of agar extracted from Gracilaria species collected along Tanzanian coast
(Elsevier, 2022) Vuai, Said A. H.
The study was conducted to investigate the effect of spatial variation, alkali treatment and the volume of extractant on yield and gel strength of agar for three Gracilaria species (G. salicornia, G. edulis and G. corticata) collected from the Tanzanian coast (Dar es Salaam, Tanga and Zanzibar). Treated and untreated G. corticata showed the highest yield (27 ± 0.7 % and 26.2 ± 1.3 % for treated and untreated, respectively), followed by G. salicornia then G. edulis. G. salicornia collected from Zanzibar showed the highest mass yield (22.9 ± 4.3 % for treated) followed by those collected from Tanga. Varying the volume for extraction showed no significant difference in mass yield where the p-value was >0.05. The highest gel strength was recorded from treated G. salicornia collected from Tanga (495 ±29.5 gcm-2). Gel strength varied significantly between species. Spatial variability showed a significant difference in gel strength; the sample collected from Tanga showed the highest gel strength, followed by Zanzibar then Dar es Salaam. The variation due to the volume of distilled water used for extraction showed no significant difference in gel strength at a p-value >0.05. The highest gel strength was recorded at the volume of 1500 mL (467.5 ±98.4 gcm-2), and the smallest gel strength was recorded at 500 mL. In all cases, there was a significant difference in mass yield and gel strength between treated and untreated samples. G. salicornia showed promising results as a local source of agar as it showed the highest gel strength though it produced an intermediate amount of agar. Based on the finding of this study, the volume of extraction of agar should be maintained as 1000 mL because by increasing the volume of extraction from 1000 mL to 1500 mL, the agar yield and gel strength don't change significantly. Agar yield and gel strength of Gracilaria species (G. salicornia, G. edulis and G. corticata) can be improved by alkali treatment, but further study is needed to determine the optimum amount and concentration of alkali to be used that will produce maximum yield and gel strength.
Characterization of atmospheric bulk deposition: implications on the quality of rainwater harvesting systems in the semi-arid city of Mekelle, northern Ethiopia
(Springer, 2016) Taffere, Getachew Redae; Beyene, Abebe; Vuai, Said A. H.; Gasana, Janvier; Seleshi, Yilma
It is estimated that about 1.2 billion people, mostly in arid and semi-arid regions of the Middle East and Africa, live in regions where water is physically scarce. Recently, rainwater harvesting and more effective water storage are suggested as important means for investment to cope against water scarcity and as an adaption to climate change. Cognizant of this fact, contribution of atmospheric deposition contaminant to rainwater harvesting systems, in the semi-arid city of Mekelle was investigated at four locations (industrial, commercial, traffic and residential areas). A total of 24 bulk samples were collected during the rainy season from May to September 2014. Physicochemical water quality analysis was performed following standard protocols. The results revealed that alkaline pH (6.95–10.29) was recorded in all the locations, with a mean pH of 8.11. The major ions analysis indicated the dominance of bicarbonates and carbonate types and to some extent sulfate and chloride type mixtures justifying the source of alkaline pH. Mean concentrations of ions follow the order of SO4 2−> Ca2+ > Mg2+ > CI−> NO3 −> Na+ > NH4 + > K. Correlation between SO4 2− and NO3 − (r = 0.436), and Mg2+ and K+ (r = 0.707) suggested their anthropogenic and crustal origin, respectively, while the correlation between NH4 + with Ca2+ and Mg2+ ascribed their role in alkalization of the rainwater. Moreover, principal component analysis showed spatiotemporal variation of atmospheric bulk components in the study area. Thus, this primary investigation demonstrated that atmospheric bulk deposition might pose public health risk due to poor rainwater quality in Mekelle city. Therefore, development of rainwater harvesting systems for semi-arid urban centers should be supplemented with low-cost water treatment technologies.
Dilemma of roof rainwater quality: Applications of physical and organic treatment methods in a water scarce region of Mekelle, Ethiopia
(Taylor & Francis, 2016) Taffere, Getachew Redae; Beyene, Abebe; Vuai, Said A. H.; Gasana, Janvier; Seleshi, Yilma
The public health field has built a body of literature showing health benefits from improvements in water quality. However, the connection between roof harvested rainwater and health is not well documented especially in developing countries. Understanding the application of locally available treatment methods provides insight into this problem. This paper reports on experimental investigations where rainwater collected from a typical domestic roof in Mekelle, Ethiopia was treated using Moringa stenopetala seed, sand filter and boiling. The quality of the raw and treated roof harvested rainwater were compared against the Ethiopian and World Health Organization drinking water standards to investigate its suitability as a supplement for potable water supply. The pollutants analysed were total coliforms and turbidity. A significant improvement of turbidity and total coliforms was observed. This implies that application of plant coagulant followed by filtration can sufficiently treat rainwater and can be used as a low-cost treatment option in water scarce areas.
Disparities in risk factors associated with obesity between Zanzibar and Tanzania mainland among women of reproductive age based on the 2010 TDHS
(Hindawi Publishing Corporation, 2016) Paul, Edwin; Mtumwa, Abdalla H.; Ntwenya, Julius Edward; Vuai, Said A. H.
The occurrence of overweight and obesity has serious health implications. The 2010 Tanzania Demographic and Health Survey data set was reanalyzed to compare the prevalence of overweight and obesity between Mainland Tanzania and Zanzibar and to determine how demographic factors can predict overweight and obesity across the United Republic of Tanzania. About 7.92% of the Tanzanian women of reproductive age were obese, 15% were overweight, and 11.5% were underweight. Women from Mainland Tanzania (6.56%) were significantly less likely (AOR = 0.66, 95% CI: 0.53–0.82) to be affected by obesity as compared to women from Zanzibar (12.19%).The common predictors of obesity in Mainland Tanzania and Zanzibar were wealth index, marital status, and age. Whereas the place of residence and education level emerged as predictors of obesity in the Mainland Tanzania alone, the number of meals per day did so in Zanzibar. Most importantly, Zanzibar had a greater prevalence of obesity compared to Mainland Tanzania.
Influence of land use activities on spatial and temporal variation of nutrient deposition in Mwanza region: implication to the atmospheric loading to the Lake Victoria
(Scientific Research, 2013) Vuai, Said A. H.; Ibembe, John D.; Mungai, Nancy W.
Increase in population growth and the associated activities have increased the nutrient input to the Lake Victoria through atmosphere and river discharge. Atmospheric input of nutrient is believed to exceed that of river discharge due to relatively higher contribution of water mass to the Lake from atmosphere. However, precipitation characteristics with respect to nutrients have not been well studied to allow qualification and quantification of atmospheric contribution to the Lake Victoria. This study was conducted to investigate influence of land use activities on spatial and temporal variation of nutrient inputs from atmosphere and to estimate atmospheric loading to the Lake Victoria. The results re- vealed that there is significant spatial and temporal variation of nutrient deposition in the study area. High concentra- tions of nutrients were observed during short rains starting from September to December. This was attributed to dissolu- tion of nutrients from soil particals and ash residues due to biomass burning accumulated in the atmosphere during dry season of June to August. Spatial variation of nutrients reflects land use activities. Urban and peri-urban areas showed very high concentration of nitrate nitrogen due to industrial and vehicle emission while rural area showed high concen- tration of phosphorous species and reduced forms of nitrogen species reflecting agricultural activities and animal keep- ing. Generally, nutrient deposition load was higher in rural area compared to urban with respective values of 15.5 and 13.9 kg·ha−1·y−1 for total nitrogen and 6.1 and 2.8 kg·ha−1·y−1 for total phosphorous. These results suggest that in order to realize significant reduction of nutrient input to the Lake Victoria, measures should be taken to control agricultural activities through proper land use planning. The measure may be directed to reduce biomass burning, emission from industries and vehicle as well as animal residue.
Location and time-specific investigation of roof rainwater quality is important to safeguard public health
(Taylor & Francis, 2016) Taffere, Getachew Redae; Beyene, Abebe; Vuai, Said A. H.; Gasana, Janvier; Seleshi, Yilma
Harvested roof rainwater plays a vital role in supplying water in the scarce semi-arid areas. Prior knowledge of rainwater quality helps to understand the relative pollutant contributions of location- and time-associated factors. The present work is aimed to explore source and time factors affecting rainwater quality and associated public health risk in the city of Mekelle, a semi-arid area in Ethiopia. Roof rainwater samples (n = 21) were collected from May to August 2014 from residential, commercial, bus station, and industrial areas. The samples were analyzed for major ions, physical parameters, and coliforms. The order of concentrations of major ions was observed to > Ca2+ > Cl− > Mg2+ > > Na+ > > > K+. The average pH of rainwater at these stations was 8.26 and ranging from 6.84 to 10.59, indicating alkaline nature. The observed alkalinity is attributed to the nature of soil and geological formation of the area and a significant influence of the cement factory. No definite trends were found in most of the ionic components at all the locations and time of sampling with p-value > 0.05. However, concentrations of physical parameters (total dissolved solids, electrical conductivity, total suspended solids, and turbidity) were statistically significant with time of sampling (p-value < 0.01). Bacteriologically, 76% of the samples were positive for total coliforms. Moreover, 19% of the samples were positive for fecal coliform. These signify the importance of appropriate treatment measures before using rainwater for domestic water supply so as to prevent potential adverse health effects.
Quantum chemical study of effect on adsorption properties of antituberculosis drug N-Cyclopentylidenepyridine-4-carbohydrazide interaction with CNT(C56H16)
(Elsevier, 2023) Pandey, Anoop Kumar; Dwivedi, Apoorva; Mishra, Avinash Kumar; Tiwari, Satyendra Nath; Singh, Vijay; Vuai, Said A. H.
Tuberculosis is the most common disease that affects the lungs in humans. The electronic structural and chemical properties of the antituberculosis drug N-Cyclopentylidenepyridine-4-carbohydrazide have already been investigated. The adsorption properties of the antituberculosis drug N-Cyclopentylidenepyridine-4-carbohydrazide (CPPC) with single-wall carbon nanotube CNT(C56H16) are investigated using a combination of DFT/B3LYP method and 6-31G(d,p) basis set in both gaseous and water solvent, and calculated results are compared. By comparing CNT's corresponding optimized bond lengths with CNT@CPPC, the effect of CPPC adsorption on optimized drug delivery system parameters has been discussed. Based on topological parameters, the nonbonding interaction between CNT and CPPC drug is discussed using QTAIM analysis at BCP in both gas and water solvent. The thermodynamical stability of the CPPC@CNT adsorption process is also calculated, showing the adsorption of CPPC with CNT favors in both media. Natural bond analysis (NBO) was used to investigate the IR spectra, and the effect of charge transfer from CPPC to CNT in CNT@CPPC in both media provides information about how polarity changes from gas to water solvent. Because drug delivery action is done in blood plasma, the UV–Vis spectra of CNT are compared to CNT@CPPC in water solvent, providing insight into the adsorption of CPPC drug by CNT. We have compared the chemical shift isotropic (CS1) and chemical shift anisotropic (CSA) of CNT, CPPC, and CNT@CPPC to determine the change in electron density.
Relaxed complex scheme and molecular dynamics simulation suggests small molecule inhibitor of human TMPRSS2 for combating COVID-19
(Taylor & Francis, 2021) Vuai, Said A. H.; Ogedjo, Marcelina M.; Isaac, Onoka; Sahini, Mtabazi G.; Swai, Hulda S.; Shadrack, Daniel M.
As the coronavirus disease 19 (COVID-19) pandemic continues to pose a health and economic crisis worldwide, the quest for drugs and/or vaccines against the virus continues. The human transmembrane protease serine 2 (TMPRSS2) has attracted attention as a target for drug discovery, as inhibition of its catalytic reaction would result in the inactivation of the proteolytic cleavage of the SARS-CoV-2 S protein. As a result, the inactivation prevents viral cell entry to the host’s cell. In this work, we screened and identified two potent molecules that interact and inhibit the catalytic reaction by using computational approaches. Two docking screening experiments were performed utilizing the crystal structure and holo ensemble structure obtained from molecular dynamics in bound form. There is enhancement and sensitivity of docking results to the holo ensemble as compared to the crystal structure. Compound 1 demonstrated a similar inhibition value to nafamostat by interacting with catalytic triad residues His296 and Ser441, thereby disrupting the already established hydrogen bond interaction. The stability of the ligand–TMPRSS2 complexes was studied by molecular dynamics simulation, and the binding energy was re-scored by using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy. The obtained compounds may serve as an initial point toward the discovery of potent TMPRSS2 inhibitors upon further in vivo validation.
Reliability analysis of roof rainwater harvesting systems in a semi-arid region of sub-Saharan Africa: Case study of Mekelle, Ethiopia
(Taylor & Francis, 2016) Taffere, Getachew Redae; Beyene, Abebe; Vuai, Said A. H.; Gasana, Janvier; Seleshi, Yilma
Curbing water scarcity problems in semi-arid regions is a top priority for economic and social development. Alternative strategies for sustainable domestic water supply are therefore required to augment water supply with affordable cost and technology. Scant research findings in sub-Saharan Africa have, however, reported inefficiency in adapting to water scarcity problems in the region. Therefore, an investigation of domestic rainwater harvesting (RWH) reliability is important to identify factors affecting the system. We found that rainwater harvesting with the existing traditional RWH systems in Mekelle city was unreliable. Unreliability was attributed to inefficient design (the systems were installed without considering deterministically the stochastic nature of rainfall), family size, water demand, rooftop area and storage tank size.
A review on contaminants of emerging concern in the environment: a focus on active chemicals in sub-Saharan Africa
(Scientific Research Publishing, Inc., 2022) Ripanda, Asha S.; Rwiza, Mwemezi Johaiven; Nyanza, Elias C.; Njau, Karoli N.; Vuai, Said A. H.; Machunda, Revocatus L.
Active chemicals are among the contaminants of emerging concern that are rarely covered in regulatory documents in sub-Saharan Africa. These substances are neither in the list of routinely monitored substances nor in the guidelines for routine environmental monitoring activities. This has been of concern to public health officials, toxicologists, communities, and governments, hence the need for risk assessment and regulation of these substances. In this review article, the presence of active chemicals in the sub-Saharan African environment was investigated. The results indicate the availability of few studies in some countries, while in other countries no reports of active chemicals were found, hence the need for further research targeting such countries. It was further observed that mixtures of active chemicals from different therapeutic categories—such as antibiotics and analgesics—were reported. The natural environment is increasingly at risk due to the presence of these substances, their metabolites, and their transformation by products. These substances are characterized by persistence as a result of their non-biodegradable nature; hence, they circulate from one environmental compartment to another through the food chain, causing harm along the way. Most studies that evaluated the toxicity of these substances considered the effects of a single drug, but observations indicated the presence of drug mixtures, hence the need for further evaluation of the effects of drug–drug interactions—including synergistic and additive effects—for environmental sustainability. The presence of ACs in several environmental compartments at quantifiable quantities was discovered in this investigation, indicating the potential for ecosystem injury as a result of bioaccumulation, bioconcentration, and biomagnification through the food chain. This necessitates further research on the subject in order to ensure a healthier environment.
Spatial variation of nutrients in Sondu-miriu and Simiyu-duma rivers: Implication on sources and factors influencing their transportation into the Lake Victoria
(OMICS Publishing Group, 2012) Ibembe, John D.; Mungai, Nancy; Vuai, Said A. H.
Lake Victoria basin has been under growing pressure from both natural and anthropogenic activities. These activities have created many nutrient pollution sources which affect the survival and sustainability of the Lake Ecosystem. This study was conducted to investigate the transportation of nutrients into the Lake Victoria through the Sondu-Miriu (SM) and the Simiyu-Duma (SD) rivers to represent the changes that have been occurring in many rivers draining the Lake basin. Water samples were collected along the SM and the SD river courses from upstream to the Lake shore. The results showed that the concentration of nitrate ranged between 770 μgL-1 and 970 μgL-1 for SM River and between 400 μgL-1 and 1250 μgL-1 for SD River while for phosphate it ranged from 120 μgL-1 to 270 μgL-1and from 457 μgL-1 to 1175 μgL-1 for SM and SD Rivers, respectively. The estimated nutrient loading through SM were 40ty-1 and 7.9ty-1 while for SD River were 25 ty-1 and 26ty-1 for dissolved inorganic nitrogen and phosphorous, respectively. The spatial variation of the concentrations nitrogen was not significant along the SM while in the SD Rivers the average concentration was lower in downstream than in the middle due to presence of swamp and dam that regulate the flow of water and retain nutrients. The results suggest that the catchment soil and rock are the major sources of the nutrients and their interaction with water dominate the transportation mechanism of the nutrients to the Lake Victoria through the Sondu-Miriu and Simiyu-Duma rivers.
Theoretical studies of electronic and optical characteristics in donor-π-Acceptor (D-π-A) dyes: DFT and TD-DFT methods
(Oxford University Press (OUP), 2023-12-25) Numbury, Surendra Babu; Khalfan, Mwanahadia Salum; Vuai, Said A. H.
This research focused on enhancing D-p-A organic dyes derived from coumarin and its derivatives, collectively referred to as D-CM-A dyes. The study aimed to improve these dyes by introducing various donors and acceptors to the coumarin structure. Six new coumarin dyes were evaluated, primarily for their potential application in dye-sensitized solar cells (DSSCs) to enhance energy efficiency. The analysis involved calculating the geometry, electronic properties, and optoelectronic characteristics of the dye molecules using DFT and TD-DFT methods with the B3LYP functional and the 6-311G basis set in both gas and solvent phases. The primary focus was to understand how modifications to the p-conjugated D-p-A organic dyes influenced their optoelectronic properties, including key factors such as maximum absorption wavelength (kmax), highest occupied molecular orbital energy (EHOMO), lowest unoccupied molecular orbital energy (ELUMO), and energy gap (Egap). Additionally, the study explored the photovoltaic properties of these dyes. The findings highlighted D4-CMA4 as a promising candidate with the narrowest energy gap, while D1-CM-A1 and D2-CM-A2 showed superior light-harvesting efficiencies (LHE) compared to other derivatives. In conclusion, this study suggests that D1-CM-A1 and D2-CM-A2 are favourable choices for enhancing the performance of DSSCs due to their promising optoelectronic properties.
Theoretical studies of optoelectronic and photovoltaic properties of D–A polymer monomers by Density Functional Theory (DFT)
(Taylor & Francis, 2021) Babu, Numbury Surendra; Vuai, Said A. H.
In this research article, the new donor–acceptor (D–A) monomers developed using 4-methoxy- 9-methyl-9 H-carbazole (MMCB) as electron donors and various electron acceptors. DFT and TDDFT methods at the level of B3LYP with a 6–311 G basis set in a gas and chloroform solvent were used to calculate electronic and optoelectronic properties. To dissect the relationship between the molecular and optoelectronic structures, the impacts of specific acceptors on the geometry of molecules and optoelectronic properties of these D–A monomers were discussed. The calculations are also carried out on HOMO–LUMO, atomic orbital densities. The calculated band gap Eg of the monomers considered increases 3,6-MMCB-OCP ≈ 3,6-MMCB-BCO < 3,6-MMCB-SDP < 3,6-MMCBSCP < 3,6-MMCB-TCP < 3,6-MMCB-TDP < 3,6-MMCB-BCS < 3,6-MMCB-BCT in both in the gas and solvent phases. Subsequently, the optoelectrical properties of EHOMO, ELUMO, Eopt, and EB energies were critically updated. Compared to different monomers, the far lower Eg of the 3,6-MMCB-OCP and 3,6-CB-BCO has shown optoelectronic applications in organic solar cells like BHJ.

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