Browsing by Author "Shahbaaz, Mohd"
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Item Antennal enriched odorant binding proteins are required for odor communication in glossina f. Fuscipes(MPDI, 2021) Diallo, Souleymane; Shahbaaz, Mohd; Makwatta, JohnMark O.Olfaction is orchestrated at different stages and involves various proteins at each step. For example, odorant-binding proteins (OBPs) are soluble proteins found in sensillum lymph that might encounter odorants before reaching the odorant receptors. In tsetse flies, the function of OBPs in olfaction is less understood. Here, we investigated the role of OBPs in Glossina fuscipes fuscipes olfaction, the main vector of sleeping sickness, using multidisciplinary approaches. Our tissue expression study demonstrated that GffLush was conserved in legs and antenna in both sexes, whereas GffObp44 and GffObp69 were expressed in the legs but absent in the antenna. GffObp99 was absent in the female antenna but expressed in the male antenna. Short odorant exposure induced a fast alteration in the transcription of OBP genes. Furthermore, we successfully silenced a specific OBP expressed in the antenna via dsRNAi feeding to decipher its function.Item Carbonic anhydrase II based biosensing of carbon dioxide at high temperature: an analytical and MD simulation study(OMICS International, 2018) Idrees, Danish; Anwer, Razique; Shahbaaz, Mohd; Sabela, Myalowenkosi; Khamees, Osama A. Al; Gourinath, Samudrala; Kumar, Manoj; Singh, M.P.; Qumaizi, Khalid I. AlConcentration of carbon dioxide (CO2) in the atmosphere has increased significantly due to anthropogenic activities and attributed as a major factor to global warming. Its detection by biosensing methods will provide an alternative for the assessment of CO2 concentration. Biomineralization of CO2 is one of the available methods for the biological conversion of CO2 to carbonate using a highly active enzyme, carbonic anhydrase II (CAII). CAII was used for the carbonation reaction to convert CO2 to CaCO3. The precipitation of calcium carbonate (CaCO3) was promoted in the presence of the CAII at 325 K. CAII showed an enhanced formation of solid CaCO3 through the acceleration of CO2 hydration rate at 325 K. Furthermore, the electrocatalytic properties of glassy carbon electrode enable us to determine the reduction peak potential values of CO2 through cyclic voltammetry at –1.75 and 0.3 V at 325 K. Molecular dynamic (MD) simulations were performed each at 50 ns time scale provided a deeper insight into the molecular basis of the CAII interaction with CO2 at different temperatures, highlighted that the CAII can detect CO2 up to 325 K. We assume that CAII could be an effective and economical biosensor for biomineralization of CO2 at high temperature 325 K.Item Cellular and molecular targets of waterbuck repellent blend odors in antennae of glossina fuscipes fuscipes newstead, 1910(Frontiers Media S.A., 2020) Diallo, Souleymane; Shahbaaz, Mohd; Torto, BaldwynInsects that transmit many of the world’s deadliest animal diseases, for instance trypanosomosis, find their suitable hosts and avoid non-preferred hosts mostly through olfactory cues. The waterbuck repellent blend (WRB) comprising geranylacetone, guaiacol, pentanoic acid, and d-octalactone derived from waterbuck skin odor is a repellent to some savannah-adapted tsetse flies and reduces trap catches of riverine species. However, the cellular and molecular mechanisms associated with detection and coding of the repellent odors remain to be elucidated. Here, we demonstrated that WRB inhibited blood feeding in both Glossina pallidipes Austen, 1903 and Glossina fuscipes fuscipes Newstead, 1910. Using the DREAM (Deorphanization of Receptors based on Expression Alterations in odorant receptor mRNA levels) technique, combined with ortholog comparison and molecular docking, we predicted the putative odorant receptors (ORs) for the WRB in G. f. fuscipes, a non-model insect.Item Computational approaches for the design of novel anticancer compounds based on pyrazolo[3,4-d]pyrimidine derivatives as trap1 inhibitor(MPDI, 2021) Ali, Amen; Abdellattif, Magda H; Shahbaaz, MohdIn the present in-silico study, various computational techniques were applied to determine potent compounds against TRAP1 kinase. The pharmacophore hypothesis DHHRR_1 consists of important features required for activity. The 3D QSAR study showed a statistically significant model with R2 = 0.96 and Q2 = 0.57. Leave one out (LOO) cross-validation (R2 CV = 0.58) was used to validate the QSAR model. The molecular docking study showed maximum XP docking scores (−11.265, −10.532, −10.422, −10.827, −10.753 kcal/mol) for potent pyrazole analogs (42, 46, 49, 56, 43), respectively, with significant interactions with amino acid residues (ASP 594, CYS 532, PHE 583, SER 536) against TRAP1 kinase receptors (PDB ID: 5Y3N). Furthermore, the docking results were validated using the 100 ns MD simulations performed for the selected five docked complexes. The selected inhibitors showed relatively higher binding affinities than the TRAP1 inhibitor molecules present in the literature. The ZINC database was used for a virtual screening study that screened ZINC05297837, ZINC05434822, and ZINC72286418, which showed similar binding interactions to those shown by potent ligands. Absorption, distribution, metabolism, and excretion (ADME) analysis showed noticeable results. The results of the study may be helpful for the further development of potent TRAP1 inhibitors.Item Corrigendum: Synthesis and cytotoxic activity of novel indole derivatives and their in silico screening on spike glycoprotein of sars-cov-2(Frontiers Media, 2021) Gobinath, Perumal; Packialakshmi, Ponnusamy; Shahbaaz, MohdThe authors Kaliappillai Vijayakumar, Magda H. Abdellattif, Mohd Shahbaaz were not included in the published article and the authors Daoud Ali, Saud Alarifi, and Amal Alotaibi were mistakenly included in the author list. The author list has been corrected throughout the article and in the Author Contributions statement. In addition, the funding information was incorrect and has been amended to include funding for Magda H. Abdellattif. The corrected Author Contributions, Funding and Acknowledgments statements appears below. The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.Item Current perspectives in the discovery of newer medications against the outbreak of Covid-19(Frontiers Media, 2021) Ramesh, M.; Anand, Krishnan; Shahbaaz, MohdA rapid and increasing spread of COVID-19 pandemic disease has been perceived worldwide in 2020. The current COVID-19 disease outbreak is due to the spread of SARS-CoV-2. SARS-CoV-2 is a new strain of coronavirus that has spike protein on the envelope. The spike protein of the virus binds with the ACE-2 receptor of the human lungs surface for entering into the host. Therefore, the blocking of viral entry into the host by targeting the spike protein has been suggested to be a valid strategy to treat COVID-19. The patients of COVID-19 were found to be asymptomatic, cold, mild to severe respiratory illness, and leading to death. The severe illness has been noted mainly in old age people, cardiovascular disease patients, and respiratory disease patients. However, the long-term health effects due to COVID-19 are not yet known. Recently, the vaccines were authorized to protect from COVID-19.Item Designing novel possible kinase inhibitor derivatives as therapeutics against Mycobacterium tuberculosis: An in silico study(Scientific Reports, 2019) Shahbaaz, Mohd; Nkaule, Anati; Christoffels, AlanRv2984 is one of the polyphosphate kinases present in Mycobacterium tuberculosis involved in the catalytic synthesis of inorganic polyphosphate, which plays an essential role in bacterial virulence and drug resistance. Consequently, the structure of Rv2984 was investigated and an 18 membered compound library was designed by altering the scaffolds of computationally identified inhibitors. The virtual screening of these altered inhibitors was performed against Rv2984 and the top three scoring inhibitors were selected, exhibiting the free energy of binding between 8.2–9 kcal mol−1 and inhibition constants in the range of 255–866 nM. These selected molecules showed relatively higher binding affinities against Rv2984 compared to the first line drugs Isoniazid and Rifampicin. Furthermore, the docked complexes were further analyzed in explicit water conditions using 100 ns Molecular Dynamics simulations. Through the assessment of obtained trajectories, the interactions between the protein and selected inhibitors including first line drugs were evaluated using MM/PBSA technique. The results validated the higher efficiency of the designed molecules compared to 1st line drugs with total interaction energies observed between −100 kJ mol−1 and −1000 kJ mol−1. This study will facilitate the process of drug designing against M. tuberculosis and can be used in the development of potential therapeutics against drug-resistant strains of bacteria.Item Functional and structural analysis of predicted proteins obtained from homo sapiens' minisatellite 33.15-tagged transcript pAKT-45 variants(Hindawi, 2020) Shahbaaz, Mohd; Al-Samghan, Awad Saeed; Alzahrani, Othman RashedThe spermatozoa are transcriptionally dormant entities which have been recognized to be an archive of mRNA, coding for a variety of functionally crucial cellular proteins. This significant repository of mRNA is predicted to be associated with early embryogenesis and postfertilization. The mRNA transcripts which are tagged with minisatellites have been involved in the regulation of the gene functions as well as their organization. However, very little information is available regarding the expression of the transcripts tagged with minisatellites in spermatozoa. Therefore, in order to understand the functions and the conformational behavior of the proteins expressed from these minisatellite-tagged transcripts, we have performed a detailed in silico analysis using the sequences of the transcripts. The protein predicted from KF274549 showed the functionalities similar to uncharacterized C4orf26 proteins, while that obtained from KF274557 predicted to be a metallophosphoesterase. Furthermore, the structural folds in the structure of these predicted proteins were analyzed by using the homology modeling and their conformational behaviors in the explicit water conditions were analyzed by using the techniques of Molecular Dynamics (MD) simulations. This detailed analysis will facilitate the understanding of these proteins in the spermatozoon region and can be used for uncovering other attributes of the metabolic network.Item In silico repurposing of a Novobiocin derivative for activity against latency associated Mycobacterium tuberculosis drug target nicotinate-nucleotide adenylyl transferase (Rv2421c)(Public Library of Science, 2021) Cloete, Ruben; Shahbaaz, Mohd; Christoffels, AlanNicotinamide-nucleotide adenylyl transferase (Rv2421c) was selected as a potential drug target, because it has been shown, in vitro, to be essential for Mycobacterium tuberculosis growth. It is conserved between mycobacterium species, is up-regulated during dormancy, has a known 3D crystal structure and has no known human homologs. A model of Rv2421c in complex with nicotinic acid adenine dinucleotide and magnesium ion was constructed and subject tovirtual ligand screening against the Prestwick Chemical Library and the ZINC database, which yielded 155 potential hit molecules. Of the 155 compounds identified five were pursued further using an IC50 based 3D-QSAR study. The 3D-QSAR model validated the inhibition properties of the five compounds based on R2 value of 0.895 and Q2 value of 0.944 compared to known inhibitors of Rv2421c. Higher binding affinities was observed for the novel ZINC13544129 and two FDA approved compounds (Novobiocin sodium salt, Sulfasalazine). Similarly, the total interaction energy was found to be the highest for Cromolyn disodium system (-418.88 kJ/mol) followed by Novobiocin (-379.19 kJ/mol) and Sulfasalazine with (-330.13 kJ/mol) compared to substrate DND having (-185.52 kJ/mol). Subsequent in vitro testing of the five compounds identified Novobiocin sodium salt with activity against Mycobacterium tuberculosis at 50 μM, 25μM and weakly at 10μM concentrations. Novobiocin salt interacts with a MG ion and active site residues His20, Thr86, Gly107 and Leu164 similar to substrate DND of Mycobacterium tuberculosis Rv2421c. Additional in silico structural analysis of known Novobiocin sodium salt derivatives against Rv2421c suggest Coumermycin as a promising alternative for the treatment of Mycobacterium tuberculosis based on large number of hydrogen bond interactions with Rv2421c similar in comparison to Novobiocin salt and substrate DND.Item Inhibiting CDK6 activity by quercetin is an attractive strategy for cancer therapy(American Chemical Society, 2020) Shahbaaz, Mohd; Yousuf, Mohd; Khan, ParvezCyclin-dependent kinase 6 (CDK6) is a potential drug target that plays an important role in the progression of different types of cancers. We performed in silico and in vitro screening of different natural compounds and found that quercetin has a high binding affinity for the CDK6 and inhibits its activity with an IC50 = 5.89 μM. Molecular docking and a 200 ns whole atom simulation of the CDK6-quercetin complex provide insights into the binding mechanism and stability of the complex. Binding parameters ascertained by fluorescence and isothermal titration calorimetry studies revealed a binding constant in the range of 107 M−1 of quercetin to the CDK6. Thermodynamic parameters associated with the formation of the CDK6−quercetin complex suggested an electrostatic interaction-driven process. The cell-based protein expression studies in the breast (MCF-7) and lung (A549) cancer cells revealed that the treatment of quercetin decreases the expression of CDK6. Quercetin also decreases the viability and colony formation potential of selected cancer cells. Moreover, quercetin induces apoptosis, by decreasing the production of reactive oxygen species and CDK6 expression. Both in silico and in vitro studies highlight the significance of quercetin for the development of anticancer leads in terms of CDK6 inhibitors.Item A novel nano therapeutic using convalescent plasma derived exosomal (CPExo) for Covid-19: A combined hyperactive immune modulation and diagnostics(Elsevier, 2021) Anand, Krishnan; Vadivalagan, Chithravel; Shahbaaz, MohdExtracellular vesicles like exosomes are important therapeutic tactics for treating COVID -19. By utilizing convalescent plasma derived exosomes (CPExo) from COVID-19 recovered persistence could accelerate the treatment strategies in the current state of affairs. Adequate literature has shown that administering the exosome to the in vivo system could be beneficial and could target the pathogens in an effective and precise manner. In this hypothesis we highlight the CPExo instead of convalescent plasma (CP), perhaps to dispense of exosomes are gratified and it’s more effectively acquired immune response conferral through antibodies. COVID-19 convalescent plasma has billions of exosomes and it has aptitudes to carry molecular constituents like proteins, lipids, RNA and DNA, etc. Moreover, exosomes are capable of recognizing antigens with adequate sensitivity and specificity. Many of these derivatives could trigger an immune modulation into the cells and act as an epigenetic inheritor response to target pathogens through RNAs. COIVID-19 resistance activated plasma-derived exosomes are either responsible for the effects of plasma beyond the contained immune antibodies or could be inhibitory.Item Oxazinethione derivatives as a precursor to pyrazolone and pyrimidine derivatives: Synthesis, biological activities, molecular modeling, adme, and molecular dynamics studies(MDPI, 2021) Shahbaaz, Mohd; Abdellattif, Magda H; Arief, M.M.H.; Hussien, M.A.In this study, we used oxazinethione as a perfect precursor to synthesize new pyrimidine and pyrazole derivatives with potent biological activities. Biological activities were determined for all compounds against A. flavus, E. coli, S. aureus, and F. moniliform. Compounds 3, 4a-b, and 5 exhibited higher activities toward A. flavus, E. coli, S. aureus, and F. moniliform; this was indicated through the MIC (minimum inhibitory concentration). At the same time, anticancer activities were determined through four cell lines, Ovcar-3, Hela, MCF-7, and LCC-MMk. The results obtained indicated that compound 5 was the most potent compound for both cell lines. Molecular docking was studied by the MOE (molecular operating environment). The in silico ADME of compounds 2 and 5 showed good pharmacokinetic properties. The present research strengthens the applicability of these compounds as encouraging anticancer and antibacterial drugs. Moreover, JAGUAR module MD simulations were carried out at about 100 ns. In addition, spectroscopic studies were carried out to establish the reactions of the synthesized structure derivatives. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Item Repurposing based identification of novel inhibitors against mmps5-mmpl5 efflux pump of Mycobacterium smegmatis: A combined in silico and in vitro study(MDPI, 2022) Shahbaaz, Mohd; Maslov, Dmitry A.; Vatlin, Aleksey A.In the current era of a pandemic, infections of COVID-19 and Tuberculosis (TB) enhance the detrimental effects of both diseases in suffering individuals. The resistance mechanisms evolving in Mycobacterium tuberculosis are limiting the efficiency of current therapeutic measures and pressurizing the stressed medical infrastructures. The bacterial efflux pumps enable the development of resistance against recently approved drugs such as bedaquiline and clofazimine. Consequently, the MmpS5-MmpL5 protein system was selected because of its role in efflux pumping of anti-TB drugs. The MmpS5-MmpL5 systems of Mycobacterium smegmatis were modelled and the virtual screening was performed using an ASINEX library of 5968 anti-bacterial compounds. The inhibitors with the highest binding affinities and QSAR based highest predicted inhibitory concentration were selected. The MmpS5-MmpL5 associated systems with BDE_26593610 and BDD_27860195 showed highest inhibitory parameters.Item Synthesis of oxygen deficient tio2 for improved photocatalytic efficiency in solar radiation(MDPI, 2021) Badmus, Kassim Olasunkanmi; Wewers, Francois; Shahbaaz, MohdThe photocatalytic activities of TiO2 have been limited mainly to absorbing in the ultraviolet spectrum which accounts for only 5% of solar radiation. High energy band gap and electron recombination in TiO2 nanoparticles are responsible for its limitations as a photocatalyst. An oxygen deficient surface can be artificially created on the titanium oxide by zero valent nano iron through the donation of its excess electrons. A visible light active TiO2 nanoparticle was synthesized in the current investigation through simple chemical reduction using sodium boro-hydride. The physical and textural properties of the synthesized oxygen deficient TiO2 photocatalyst was measured using scanning/ transmission electron microscopy while FTIR, XRD and nitrogen sorption methods (BET) were employed for its further characterizations. Photochemical decoloration of orange II sodium dye solution in the presence of the synthesized TiO2 was measured using an UV spectrophotometer. The resulting oxygen deficient TiO2 has a lower energy band-gap, smaller pore sizes, and enhanced photo-catalytic properties.Item Transcriptomic profile of mycobacterium smegmatis in response to an imidazo[1,2-b][1,2,4,5]tetrazine reveals its possible impact on iron metabolism(Frontiers Media, 2021) Vatlin, Aleksey A.; Shitikov, Egor A.; Shahbaaz, MohdTuberculosis (TB), caused by the Mycobacterium tuberculosis complex bacteria, is one of the most pressing health problems. The development of new drugs and new therapeutic regimens effective against the pathogen is one of the greatest challenges in the way of tuberculosis control. Imidazo[1,2-b][1,2,4,5]tetrazines have shown promising activity against M. tuberculosis and M. smegmatis strains. Mutations in MSMEG_1380 lead to mmpS5–mmpL5 operon overexpression, which provides M. smegmatis with efflux-mediated resistance to imidazo[1,2-b][1,2,4,5]tetrazines, but the exact mechanism of action of these compounds remains unknown. To assess the mode of action of imidazo[1,2-b][1,2,4,5]tetrazines, we analyzed the transcriptomic response of M. smegmatis to three different concentrations of 3a compound: 1/8×, 1/4×, and 1/2× MIC. Six groups of genes responsible for siderophore synthesis and transport were upregulated in a dose-dependent manner, while virtual docking revealed proteins involved in siderophore synthesis as possible targets for 3a.