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Lanrewaju AA, Enitan-Folami AM, Nyaga MM, Sabiu S, Swalaha FM. Metabolites profiling and cheminformatics bioprospection of selected medicinal plants against the main protease and RNA-dependent RNA polymerase of SARS-CoV-2. J Biomol Struct Dyn 2024; 42:6740-6760. [PMID: 37464870 DOI: 10.1080/07391102.2023.2236718] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/08/2023] [Indexed: 07/20/2023]
Abstract
Despite the existence of some vaccines, SARS-CoV-2 (S-2) infections persist for various reasons relating to vaccine reluctance, rapid mutation rate, and an absence of specific treatments targeted to the infection. Due to their availability, low cost and low toxicity, research into potentially repurposing phytometabolites as therapeutic alternatives has gained attention. Therefore, this study explored the antiviral potential of metabolites of some medicinal plants [Spondias mombin, Macaranga barteri and Dicerocaryum eriocarpum (Sesame plant)] identified using liquid chromatography-mass spectrometry (LCMS) as possible inhibitory agents against the S-2 main protease (S-2 MP) and RNA-dependent RNA polymerase (RP) using computational approaches. Molecular docking was used to identify the compounds with the best affinities for the selected therapeutics targets. Afterwards, compounds with poor physicochemical characteristics, pharmacokinetics, and drug-likeness were screened out. The top-ranked compounds were further subjected to a 120-ns molecular dynamics (MD) simulation. Only quercetin 3-O-rhamnoside (-48.77 kcal/mol) had higher binding free energy than the reference standard (zafirlukast) (-44.99 kcal/mol) against S-2 MP. Conversely, all the top-ranked compounds (ellagic acid hexoside, spiraeoside, apigenin-4'-glucoside and chrysoeriol 7-glucuronide) except gnetin L (-24.24 kcal/mol) had higher binding free energy (-55.19 kcal/mol, -52.75 kcal/mol, -47.22 kcal/mol and -43.35 kcal/mol) respectively, against S-2 RP relative to the reference standard (-34.79 kcal/mol). The MD simulations study further revealed that the investigated inhibitors are thermodynamically stable and form structurally compatible complexes that impede the regular operation of the respective S-2 therapeutic targets. Although, these S-2 therapeutic candidates are promising, further in vitro and in vivo evaluation is required and highly recommended.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adedayo Ayodeji Lanrewaju
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
| | | | - Martin M Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
| | - Feroz Mahomed Swalaha
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
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2
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Aribisala JO, S'thebe NW, Sabiu S. In silico exploration of phenolics as modulators of penicillin binding protein (PBP) 2× of Streptococcus pneumoniae. Sci Rep 2024; 14:8788. [PMID: 38627456 PMCID: PMC11021432 DOI: 10.1038/s41598-024-59489-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
Infections caused by multidrug-resistant Streptococcus pneumoniae remain the leading cause of pneumonia-related deaths in children < 5 years globally, and mutations in penicillin-binding protein (PBP) 2 × have been identified as the major cause of resistance in the organism to beta-lactams. Thus, the development of new modulators with enhanced binding of PBP2x is highly encouraged. In this study, phenolics, due to their reported antibacterial activities, were screened against the active site of PBP2x using structure-based pharmacophore and molecular docking techniques, and the ability of the top-hit phenolics to inhibit the active and allosteric sites of PBP2x was refined through 120 ns molecular dynamic simulation. Except for gallocatechin gallate and lysidicichin, respectively, at the active and allosteric sites of PBP2x, the top-hit phenolics had higher negative binding free energy (ΔGbind) than amoxicillin [active site (- 19.23 kcal/mol), allosteric site (- 33.75 kcal/mol)]. Although silicristin had the best broad-spectrum effects at the active (- 38.41 kcal/mol) and allosteric (- 50.54 kcal/mol) sites of PBP2x, the high thermodynamic entropy (4.90 Å) of the resulting complex might suggest the need for its possible structural refinement for enhanced potency. Interestingly, silicristin had a predicted synthetic feasibility score of < 5 and quantum calculations using the DFT B3LYP/6-31G+ (dp) revealed that silicristin is less stable and more reactive than amoxicillin. These findings point to the possible benefits of the top-hit phenolics, and most especially silicristin, in the direct and synergistic treatment of infections caused by S. pneumoniae. Accordingly, silicristin is currently the subject of further confirmatory in vitro research.
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Affiliation(s)
- Jamiu Olaseni Aribisala
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Nosipho Wendy S'thebe
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa.
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Aribisala JO, Sabiu S. Cheminformatics identification of phenolics as modulators of penicillin-binding protein-3 of Pseudomonas aeruginosa towards interventive antibacterial therapy. J Biomol Struct Dyn 2024; 42:298-313. [PMID: 36974951 DOI: 10.1080/07391102.2023.2192808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/11/2023] [Indexed: 03/29/2023]
Abstract
Antibacterial resistance to β-lactams in microorganisms has been attributed majorly to alterations in penicillin-binding proteins (PBPs) coupled with β-lactams' inactivation by β-lactamase. Consequently, the identification of a novel class of therapeutics with improved modulatory action on the PBPs is imperative and plant secondary metabolites, including phenolics, have found relevance in this regard. For the first time in this study, the over 10,000 phenolics currently known were computationally evaluated against PBP3 of Pseudomonas aeruginosa, a superbug implicated in several nosocomial infections. In doing this, a library of phenolics with an affinity for PBP3 of P. aeruginosa was screened using structure-activity relationship-based pharmacophore and molecular docking approaches. Subsequent thermodynamic screening of the top five phenolics with higher docking scores, more drug-likeness attributes, and feasible synthetic accessibility was achieved through a 120 ns molecular dynamic (MD) simulation. Four of the top five hits had higher binding free energy than cefotaxime (-18.72 kcal/mol), with catechin-3-rhamside having the highest affinity (-28.99 kcal/mol). All the hits were stable at the active site of the PBP3, with catechin-3-rhamside being the most stable (2.14 Å), and established important interactions with Ser294, implicated in the catalytic activity of PBP3. Also, PBP3 became more compact with less fluctuation of the active site amino acid residues following the binding of the hits. These observations are indicative of the potential of the test compounds as PBP3 inhibitors, with catechin-3-rhamside being the most prominent of the compounds that could be further improved for enhanced druggability against PBP3 in vitro and in vivo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jamiu Olaseni Aribisala
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
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Akoonjee A, Lanrewaju AA, Balogun FO, Makunga NP, Sabiu S. Waste to Medicine: Evidence from Computational Studies on the Modulatory Role of Corn Silk on the Therapeutic Targets Implicated in Type 2 Diabetes Mellitus. BIOLOGY 2023; 12:1509. [PMID: 38132335 PMCID: PMC10740667 DOI: 10.3390/biology12121509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is characterized by insulin resistance and/or defective insulin production in the human body. Although the antidiabetic action of corn silk (CS) is well-established, the understanding of the mechanism of action (MoA) behind this potential is lacking. Hence, this study aimed to elucidate the MoA in different samples (raw and three extracts: aqueous, hydro-ethanolic, and ethanolic) as a therapeutic agent for the management of T2DM using metabolomic profiling and computational techniques. Ultra-performance liquid chromatography-mass spectrometry (UP-LCMS), in silico techniques, and density functional theory were used for compound identification and to predict the MoA. A total of 110 out of the 128 identified secondary metabolites passed the Lipinski's rule of five. The Kyoto Encyclopaedia of Genes and Genomes pathway enrichment analysis revealed the cAMP pathway as the hub signaling pathway, in which ADORA1, HCAR2, and GABBR1 were identified as the key target genes implicated in the pathway. Since gallicynoic acid (-48.74 kcal/mol), dodecanedioc acid (-34.53 kcal/mol), and tetradecanedioc acid (-36.80 kcal/mol) interacted well with ADORA1, HCAR2, and GABBR1, respectively, and are thermodynamically stable in their formed compatible complexes, according to the post-molecular dynamics simulation results, they are suggested as potential drug candidates for T2DM therapy via the maintenance of normal glucose homeostasis and pancreatic β-cell function.
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Affiliation(s)
- Ayesha Akoonjee
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
| | - Adedayo Ayodeji Lanrewaju
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
| | - Fatai Oladunni Balogun
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
| | - Nokwanda Pearl Makunga
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa;
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
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Sulyman AO, Aje OO, Ajani EO, Abdulsalam RA, Balogun FO, Sabiu S. Bioprospection of Selected Plant Secondary Metabolites as Modulators of the Proteolytic Activity of Plasmodium falciparum Plasmepsin V. BIOMED RESEARCH INTERNATIONAL 2023; 2023:6229503. [PMID: 37388365 PMCID: PMC10307063 DOI: 10.1155/2023/6229503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023]
Abstract
Malaria is a devastating disease, and its management is only achieved through chemotherapy. However, resistance to available medication is still a challenge; therefore, there is an urgent need for the discovery and development of therapeutics with a novel mechanism of action to counter the resistance scourge consistent with the currently available antimalarials. Recently, plasmepsin V was validated as a therapeutic target for the treatment of malaria. The pepsin-like aspartic protease anchored in the endoplasmic reticulum is responsible for the trafficking of parasite-derived proteins to the erythrocytic surface of the host cells. In this study, a small library of compounds was preliminarily screened in vitro to identify novel modulators of Plasmodium falciparum plasmepsin V (PfPMV). The results obtained revealed kaempferol, quercetin, and shikonin as possible PfPMV inhibitors, and these compounds were subsequently probed for their inhibitory potentials using in vitro and in silico methods. Kaempferol and shikonin noncompetitively and competitively inhibited the specific activity of PfPMV in vitro with IC50 values of 22.4 and 43.34 μM, respectively, relative to 62.6 μM obtained for pepstatin, a known aspartic protease inhibitor. Further insight into the structure-activity relationship of the compounds through a 100 ns molecular dynamic (MD) simulation showed that all the test compounds had a significant affinity for PfPMV, with quercetin (-36.56 kcal/mol) being the most prominent metabolite displaying comparable activity to pepstatin (-35.72 kcal/mol). This observation was further supported by the compactness and flexibility of the resulting complexes where the compounds do not compromise the structural integrity of PfPMV but rather stabilized and interacted with the active site amino acid residues critical to PfPMV modulation. Considering the findings in this study, quercetin, kaempferol, and shikonin could be proposed as novel aspartic protease inhibitors worthy of further investigation in the treatment of malaria.
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Affiliation(s)
- Abdulhakeem Olarewaju Sulyman
- Department of Biochemistry, Faculty of Pure and Applied Sciences, Kwara State University, P.M.B. 1530, Malete, Ilorin, Nigeria
| | - Oluwapelumi Oluwaseun Aje
- Department of Biochemistry, Faculty of Pure and Applied Sciences, Kwara State University, P.M.B. 1530, Malete, Ilorin, Nigeria
| | - Emmanuel Oladipo Ajani
- Department of Biochemistry, Faculty of Pure and Applied Sciences, Kwara State University, P.M.B. 1530, Malete, Ilorin, Nigeria
| | - Rukayat Abiola Abdulsalam
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Fatai Oladunni Balogun
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
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Astaxanthin: A promising therapeutic agent for organ fibrosis. Pharmacol Res 2023; 188:106657. [PMID: 36682437 DOI: 10.1016/j.phrs.2023.106657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/01/2023] [Accepted: 01/10/2023] [Indexed: 01/22/2023]
Abstract
Fibrosis is the end-stage pathological manifestation of many chronic diseases. Infiltration of inflammatory cells and activation of myofibroblasts are the most prominent features of fibrosis, with excessive deposition of extracellular matrix (ECM) in tissues leading to organ tissue damage, which eventually progresses to organ failure and leads to high mortality rates. At present, a large number of studies have been conducted on tissue fibrosis, and the pathological mechanism of fibrosis development has generally been recognized. However, the prevention and treatment of fibrosis is still an unsolved problem, and a shortage of drugs that can be used in the clinic persists. Astaxanthin (ASTX), a carotenoid, is widely known for its strong antioxidant capacity. ASTX also has other biological properties, such as anti-inflammatory, antiaging and anticancer properties. Recently, many papers have reported that ASTX inhibits the occurrence and development of fibrosis by regulating signaling molecular pathways, such as transforming growth factor-β/small mother against decapentaplegic protein (TGF-β1/Smad), sirtuin 1 (SIRT1), nuclear factor kappa-B (NF-κB), microRNA, nuclear factor-E2-related factor 2/antioxidant response element (Nrf 2/ARE) and reactive oxygen species (ROS) pathways. By targeting these molecular signaling pathways, ASTX may become a potential drug for the treatment of fibrotic diseases. In this review, we summarize the therapeutic effects of ASTX on organ fibrosis and its underlying mechanisms of action. By reviewing the results from in vitro and in vivo studies, we analyzed the therapeutic prospects of ASTX for various fibrotic diseases and provided insights into and strategies for exploring new drugs for the treatment of fibrosis.
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Oliyaei N, Moosavi-Nasab M, Tanideh N, Iraji A. Multiple roles of fucoxanthin and astaxanthin against Alzheimer's disease: Their pharmacological potential and therapeutic insights. Brain Res Bull 2023; 193:11-21. [PMID: 36435362 DOI: 10.1016/j.brainresbull.2022.11.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 11/24/2022]
Abstract
Alzheimer's disease (AD) is the most devastating neurodegenerative disorder affecting the elderly. The exact pathology of AD is not yet fully understood and several hallmarks such as the deposition of amyloid-β, tau hyperphosphorylation, and neuroinflammation, as well as mitochondrial, metal ions, autophagy, and cholinergic dysfunctions are known as pathologic features of AD. Since no definitive treatment has been proposed to target AD to date, many natural products have shown promising preventive potentials and contributed to slowing down the disease progression. Algae is a promising source of novel bioactive substances known to prevent neurodegenerative disorders including AD. In this context, fucoxanthin and astaxanthin, natural carotenoids abundant in algae, has shown to possess neuroprotective properties through antioxidant, and anti-inflammatory characteristics in modulating the symptoms of AD. Fucoxanthin and astaxanthin exhibit anti-AD activities by inhibition of AChE, BuChE, BACE-1, and MAO, suppression of Aβ accumulation. Also, fucoxanthin and astaxanthin inhibit apoptosis induced by Aβ1-42 and H2O2-induced cytotoxicity, and modulate the antioxidant enzymes (SOD and CAT), through inhibition of the ERK pathway. Moreover, cellular and animal studies on the beneficial effects of fucoxanthin and astaxanthin against AD were also reviewed. The potential role of fucoxanthin and astaxanthin exhibits great efficacy for the management of AD by acting on multiple targets.
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Affiliation(s)
- Najmeh Oliyaei
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Seafood Processing Research Center, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Marzieh Moosavi-Nasab
- Seafood Processing Research Center, School of Agriculture, Shiraz University, Shiraz, Iran; Department of Food Science and Technology, School of Agriculture, Shiraz University, Shiraz, Iran.
| | - Nader Tanideh
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Iraji
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Central Research laboratory, Shiraz University of Medical Sciences, Shiraz, Iran.
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Shode FO, Uhomoibhi JOO, Idowu KA, Sabiu S, Govender KK. Molecular Dynamics Study on Selected Bioactive Phytochemicals as Potential Inhibitors of HIV-1 Subtype C Protease. Metabolites 2022; 12:1155. [PMID: 36422295 PMCID: PMC9695624 DOI: 10.3390/metabo12111155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/05/2022] [Accepted: 11/15/2022] [Indexed: 09/21/2023] Open
Abstract
Acquired immunodeficiency syndrome (AIDS), one of the deadliest global diseases, is caused by the Human Immunodeficiency Virus (HIV). To date, there are no known conventional drugs that can cure HIV/AIDS, and this has prompted continuous scientific efforts in the search for novel and potent anti-HIV therapies. In this study, molecular dynamics simulation (MDS) and computational techniques were employed to investigate the inhibitory potential of bioactive compounds from selected South African indigenous plants against HIV-1 subtype C protease (HIVpro). Of the eight compounds (CMG, MA, UA, CA, BA, UAA, OAA and OA) evaluated, only six (CMG (-9.9 kcal/mol), MA (-9.3 kcal/mol), CA (-9.0 kcal/mol), BA (-8.3 kcal/mol), UAA (-8.5 kcal/mol), and OA (-8.6 kcal/mol)) showed favourable activities against HIVpro and binding landscapes like the reference FDA-approved drugs, Lopinavir (LPV) and Darunavir (DRV), with CMG and MA having the highest binding affinities. Using the structural analysis (root-mean-square deviation (RMSD), fluctuation (RMSF), and radius of gyration (RoG) of the bound complexes with HIVpro after 350 ns, structural evidence was observed, indicating that the six compounds are potential lead candidates for inhibiting HIVpro. This finding was further corroborated by the structural analysis of the enzyme-ligand complexe systems, where structural mechanisms of stability, flexibility, and compactness of the study metabolites were established following binding with HIVpro. Furthermore, the ligand interaction plots revealed that the metabolites interacted hydrophobically with the active site amino residues, with identification of other key residues implicated in HIVpro inhibition for drug design. Overall, this is the first computational report on the anti-HIV-1 activities of CMG and MA, with efforts on their in vitro and in vivo evaluations underway. Judging by the binding affinity, the degree of stability, and compactness of the lead metabolites (CMG, MA, CA, BA, OA, and UAA), they could be concomitantly explored with conventional HIVpro inhibitors in enhancing their therapeutic activities against the HIV-1 serotype.
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Affiliation(s)
- Francis Oluwole Shode
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology (DUT), P.O. Box 1334, Durban 4000, South Africa
| | - John Omo-osagie Uhomoibhi
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology (DUT), P.O. Box 1334, Durban 4000, South Africa
| | - Kehinde Ademola Idowu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology (DUT), P.O. Box 1334, Durban 4000, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology (DUT), P.O. Box 1334, Durban 4000, South Africa
| | - Krishna Kuben Govender
- Department of Chemical Sciences, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg 2028, South Africa
- National Institute for Theoretical and Computational Sciences, NITHeCS, Stellenbosch 7602, South Africa
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The Role of Astaxanthin as a Nutraceutical in Health and Age-Related Conditions. Molecules 2022; 27:molecules27217167. [PMID: 36363994 PMCID: PMC9655540 DOI: 10.3390/molecules27217167] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 01/24/2023] Open
Abstract
The current review provides an up-to-date analysis of scientific data on astaxanthin (ASX) sources and experimental studies on its health benefits as a potent antioxidant in the aging process. ASX is a liposoluble carotenoid nutrient and reddish-orange pigment, naturally synthesized by numerous microalgae, yeasts, and bacteria as secondary metabolites. Provides a reddish hue to redfish and shellfish flesh that feed on ASX-producing microorganisms. The microalga Haematococcus pluvialis is the most important source for its industrial bioproduction. Due to its strong antioxidant properties, numerous investigations reported that natural ASX is a more significant antioxidant agent than other antioxidants, such as vitamin C, vitamin E, and β-carotene. Furthermore, several data show that ASX possesses important nutraceutical applications and health benefits, especially in healthy aging processes. However, further studies are needed for a deeper understanding of the potential mechanisms through which ASX could lead to its effective role in the healthy aging process, such as supporting brain health and skin homeostasis. This review highlights the current investigations on the effective role of ASX in oxidative stress, aging mechanisms, skin physiology, and central nervous system functioning, and shows the potential clinical implications related to its consumption.
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Aribisala JO, Sabiu S. Redox Impact on Bacterial Macromolecule: A Promising Avenue for Discovery and Development of Novel Antibacterials. Biomolecules 2022; 12:1545. [PMID: 36358894 PMCID: PMC9688007 DOI: 10.3390/biom12111545] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/20/2022] [Accepted: 10/20/2022] [Indexed: 07/30/2023] Open
Abstract
Antibiotic resistance in bacteria has remained a serious public health concern, resulting in substantial deaths and morbidity each year. Factors such as mutation and abuse of currently available antibiotics have contributed to the bulk of the menace. Hence, the introduction and implementation of new therapeutic strategies are imperative. Of these strategies, data supporting the role of reactive oxygen species (ROS) in bacterial lethality are intriguing, with several antimicrobials, including antibiotics such as fluoroquinolones, β-lactams, and aminoglycosides, as well as natural plant compounds, being remarkably implicated. Following treatment with ROS-inducing antimicrobials, ROS such as O2•-, •OH, and H2O2 generated in bacteria, which the organism is unable to detoxify, damage cellular macromolecules such as proteins, lipids, and nucleic acids and results in cell death. Despite the unique mechanism of action of ROS-inducing antibacterials and significant studies on ROS-mediated means of bacterial killing, the field remains a topical one, with contradicting viewpoints that require frequent review. Here, we appraised the antibacterial agents (antibiotics, natural and synthetic compounds) implicated in ROS generation and the safety concerns associated with their usage. Further, background information on the sources and types of ROS in bacteria, the mechanism of bacterial lethality via oxidative stress, as well as viewpoints on the ROS hypothesis undermining and solidifying this concept are discussed.
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Idowu KA, Onyenaka C, Olaleye OA. A computational evaluation of structural stability of omicron and delta mutations of SARS-CoV-2 spike proteins and human ACE-2 interactions. INFORMATICS IN MEDICINE UNLOCKED 2022; 33:101074. [PMID: 36092780 PMCID: PMC9450468 DOI: 10.1016/j.imu.2022.101074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/04/2022] Open
Abstract
Several more infectious SARS-CoV-2 variants have emerged globally since SARS-CoV-2 pandemic and the discovery of the first D614G variant of SARS-CoV-2 spike proteins in 2020. Delta (B.1.617.2) and Omicron (B.1.1.529) variants have proven to be of major concern out of all the reported variants, considering their influence on the virus' transmissibility and severity. This study aimed at evaluating the impact of mutations on these two variants on stability and molecular interactions between the viral Spike protein and human angiotensin converting enzyme-2 (hACE-2). The spike proteins receptor binding domain (RBD) was docked with the hACE-2 using HADDOCK servers. To understand and establish the effects of the mutations on the structural stability and flexibility of the RBD-hACE-2 complex, molecular dynamic (MD) simulation of the docked complex was performed and evaluated. The findings from both molecular docking analysis and binding free energy showed that the Omicron (OM) variant has high receptiveness towards hACE-2 versus Delta variant (DT), thereby, responsible for its increase in transmission. The structural stability and flexibility evaluation of variants' systems showed that mutations on DT and OM variants disturbed the stability of either the spike protein or the RBD-hACE-2 complex, with DT variant having greater instability impact. This study, therefore, assumed this obvious instability observed in DT variant might be associated or responsible for the reported severity in DT variant disease over the OM variant disease. This study provides molecular insight into the effects of OM and DT variants on stability and interactions between SARS-CoV-2 protein and hACE-2.
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Affiliation(s)
- Kehinde A Idowu
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, 3100 Cleburne St, Houston, TX, 77004, USA
| | - Collins Onyenaka
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, 3100 Cleburne St, Houston, TX, 77004, USA
| | - Omonike A Olaleye
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University, 3100 Cleburne St, Houston, TX, 77004, USA
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Molecular modeling identification of potential drug candidates from selected African plants against SARS-CoV-2 key druggable proteins. SCIENTIFIC AFRICAN 2022; 17:e01279. [PMID: 35856008 PMCID: PMC9279166 DOI: 10.1016/j.sciaf.2022.e01279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/13/2022] [Accepted: 07/10/2022] [Indexed: 01/18/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is one of the major health threats the world has experienced. In order to stem the tide of the virus and its associated disease, rapid efforts have been dedicated to identifying credible anti-SARS-CoV-2 drugs. This study forms part of the continuing efforts to develop anti-SARS-CoV-2 molecules and employed a computational structure-activity relationship approach with emphasis on 99 plant secondary metabolites from eight selected African medicinal plants with proven therapeutic benefits against respiratory diseases focusing on the viral protein targets [Spike protein (Sgp), Main protease (Mpro), and RNA-dependent RNA polymerase (RdRp)]. The results of the molecular dynamics simulation of the best docked compounds presented as binding free energy revealed that three compounds each against the Sgp (VBS, COG and ABA), and Mpro (COR, QOR and ABG) had higher and better affinity for the proteins than the respective reference drugs, cefoperazone (CSP) and Nelfinavir (NEF), while four compounds (HDG, VBS, COR and KOR) had higher and favorable binding affinity towards RdRp than the reference standard, ramdesivir (RDS). Analysis of interaction with the receptor binding domain amino acid residues of Sgp showed that VBS had the highest number of interactions (17) relative to 14 and 13 for COG and ABA, respectively. For Mpro, COR showed interactions with catalytic dyad residues (His172 and Cys145). Compared to RDS, COR, HDG, VBS and KOR formed 19, 18, 17 and 12 H-bond and Van der Waal bonds, respectively, with RdRp. Furthermore, structural examination of the three proteins after binding to the lead compounds revealed that the compounds formed stable complexes. These observations suggest that the identified compounds might be beneficial in the fight against COVID-19 and are suggested for further in vitro and in vivo experimental validation.
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Aribisala JO, Sabiu S. Cheminformatics Identification of Phenolics as Modulators of Penicillin-Binding Protein 2a of Staphylococcus aureus: A Structure–Activity-Relationship-Based Study. Pharmaceutics 2022; 14:pharmaceutics14091818. [PMID: 36145565 PMCID: PMC9503099 DOI: 10.3390/pharmaceutics14091818] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 01/16/2023] Open
Abstract
The acquisition of penicillin-binding protein (PBP) 2a in resistant strains of Staphylococcus aureus allows for the continuous production of cell walls even after the inactivation of intrinsic PBPs. Thus, the discovery of novel therapeutics with enhanced modulatory activity on PBP2a is crucial, and plant secondary metabolites, such as phenolics, have found relevance in this regard. In this study, using computational techniques, phenolics were screened against the active site of PBP2a, and the ability of the lead phenolics to modulate PBP2a’s active and allosteric sites was studied. The top-five phenolics (leads) identified through structure–activity-based screening, pharmacokinetics and synthetic feasibility evaluations were subjected to molecular dynamics simulations. Except for propan-2-one at the active site, the leads had a higher binding free energy at both the active and allosteric sites of PBP2a than amoxicillin. The leads, while promoting the thermodynamic stability of PBP2a, showed a more promising affinity at the allosteric site than the active site, with silicristin (−25.61 kcal/mol) and epicatechin gallate (−47.65 kcal/mol) having the best affinity at the active and allosteric sites, respectively. Interestingly, the modulation of Tyr446, the active site gatekeeper residue in PBP2a, was noted to correlate with the affinity of the leads at the allosteric site. Overall, these observations point to the leads’ ability to inhibit PBP2a, either directly or through allosteric modulation with conventional drugs. Further confirmatory in vitro studies on the leads are underway.
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Uhomoibhi JOO, Shode FO, Idowu KA, Sabiu S. Molecular modelling identification of phytocompounds from selected African botanicals as promising therapeutics against druggable human host cell targets of SARS-CoV-2. J Mol Graph Model 2022; 114:108185. [PMID: 35430474 PMCID: PMC9002601 DOI: 10.1016/j.jmgm.2022.108185] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 12/25/2022]
Abstract
The coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is highly pathogenic and transmissible. It is mediated by the binding of viral spike proteins to human cells via entry and replication processes involving human angiotensin converting enzyme-2 (hACE2), transmembrane serine protease (TMPRSS2) and cathepsin L (Cath L). The identification of novel therapeutics that can modulate viral entry or replication has been of research interest and would be germane in managing COVID-19 subjects. This study investigated the structure-activity relationship inhibitory potential of 99 phytocompounds from selected African botanicals with proven therapeutic benefits against respiratory diseases focusing on SARS-CoV-2's human cell proteins (hACE2, TMPRSS2, and Cathepsin L) as druggable targets using computational methods. Evaluation of the binding energies of the phytocompounds showed that two compounds, Abrusoside A (-63.393 kcal/mol) and Kaempferol-3-O-rutinoside (-58.939 kcal/mol) had stronger affinity for the exopeptidase site of hACE2 compared to the reference drug, MLN-4760 (-54.545 kcal/mol). The study further revealed that Verbascoside (-63.338 kcal/mol), Abrectorin (-37.880 kcal/mol), and Friedelin (-36.989 kcal/mol) are potential inhibitors of TMPRSS2 compared to Nafamostat (-36.186 kcal/mol), while Hemiphloin (-41.425 kcal/mol), Quercetin-3-O-rutinoside (-37.257 kcal/mol), and Myricetin-3-O-galactoside (-36.342 kcal/mol) are potential inhibitors of Cathepsin L relative to Bafilomycin A1 (-38.180 kcal/mol). The structural analysis suggests that these compounds do not compromise the structural integrity of the proteins, but rather stabilized and interacted well with the active site amino acid residues critical to inhibition of the respective proteins. Overall, the findings from this study are suggestive of the structural mechanism of inhibitory action of the identified leads against the proteins critical for SARS-CoV-2 to enter the human host cell. While the study has lent credence to the significant role the compounds could play in developing potent SARS-CoV-2 candidate drugs against COVID-19, further structural refinement, and modifications of the compounds for subsequent in vitro as well as preclinical and clinical evaluations are underway.
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Affiliation(s)
- John Omo-Osagie Uhomoibhi
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Francis Oluwole Shode
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Kehinde Ademola Idowu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa.
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Orientin Enhances Colistin-Mediated Bacterial Lethality through Oxidative Stress Involvement. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:3809232. [PMID: 35586695 PMCID: PMC9110166 DOI: 10.1155/2022/3809232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022]
Abstract
Bacterial resistance to colistin has prompted the search for alternative strategies to enhance antibacterial potential. Combination therapy remains one of the viable strategies in antibacterial therapy and has been proven to be effective in reducing the risk of resistance. In this study, the potential of orientin for enhancing the antibacterial activity of colistin was assessed against Klebsiella pneumoniae and Pseudomonas aeruginosa in vitro. The involvement of oxidative stress in such enhancement was also assessed. The minimum inhibitory concentrations (MICs) of colistin and orientin were 16 μg/mL and 64 μg/mL against K. pneumoniae and 64 μg/mL and 256 μg/mL against P. aeruginosa respectively. For the combination therapy, orientin potentiates the antibacterial effect of colistin with a friction inhibitory concentration index (FICI) of 0.37 and 0.31 against K. pneumoniae and P. aeruginosa, respectively. This observation suggests a synergistic interaction, with the MIC of colistin being reduced by 3- and 4-fold in the presence of orientin against K. pneumoniae and P. aeruginosa, respectively. Additionally, treatment with the combination of colistin and orientin induced oxidative stress against both organisms through increased cellular levels of superoxide anion radicals with concomitant increase in NAD+/NADH and ADP/ATP ratios. These findings suggest that orientin enhanced colistin in the killing of the test bacteria and the cotreatment of colistin and orientin induced oxidative stress, through reactive oxygen species generation, which consequently facilitated bacterial lethality without causing drug-drug interactions. Although, the data presented in this study has supported the capability of orientin for strengthening antibacterial activity of colistin toward the fight against drug-resistant Gram-negative bacteria, studies focusing on the exact target and mechanism of action of orientin are underway.
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Elumalai E, Suresh Kumar M. Identification of neo-andrographolide compound targeting NS1 Lys14: an important residue in NS1 activity driving dengue pathogenesis. J Biomol Struct Dyn 2022:1-11. [DOI: 10.1080/07391102.2022.2068073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Elakkiya Elumalai
- Center for Bioinformatics, Pondicherry University, Pondicherry, India
| | - M. Suresh Kumar
- Center for Bioinformatics, Pondicherry University, Pondicherry, India
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Astaxanthin from Crustaceans and Their Byproducts: A Bioactive Metabolite Candidate for Therapeutic Application. Mar Drugs 2022; 20:md20030206. [PMID: 35323505 PMCID: PMC8955251 DOI: 10.3390/md20030206] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 12/12/2022] Open
Abstract
In recent years, the food, pharma, and cosmetic industries have shown considerable interest in bioactive molecules of marine origin that show high potential for application as nutraceuticals and therapeutic agents. Astaxanthin, a lipid-soluble and orange-reddish-colored carotenoid pigment, is one of the most investigated pigments. Natural astaxanthin is mainly produced from microalgae, and it shows much stronger antioxidant properties than its synthetic counterpart. This paper aims to summarize and discuss the important aspects and recent findings associated with the possible use of crustacean byproducts as a source of astaxanthin. In the last five years of research on the crustaceans and their byproducts as a source of natural astaxanthin, there are many new findings regarding the astaxanthin content in different species and new green extraction protocols for its extraction. However, there is a lack of information on the amounts of astaxanthin currently obtained from the byproducts as well as on the cost-effectiveness of the astaxanthin production from the byproducts. Improvement in these areas would most certainly contribute to the reduction of waste and reuse in the crustacean processing industry. Successful exploitation of byproducts for recovery of this valuable compound would have both environmental and social benefits. Finally, astaxanthin’s strong biological activity and prominent health benefits have been discussed in the paper.
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Rampadarath A, Balogun FO, Pillay C, Sabiu S. Identification of Flavonoid C-Glycosides as Promising Antidiabetics Targeting Protein Tyrosine Phosphatase 1B. J Diabetes Res 2022; 2022:6233217. [PMID: 35782627 PMCID: PMC9249544 DOI: 10.1155/2022/6233217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 06/08/2022] [Indexed: 12/15/2022] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B), a negative regulator of the insulin signaling pathway, has gained attention as a validated druggable target in the management of type 2 diabetes mellitus (T2DM). The lack of clinically approved PTP1B inhibitors has continued to prompt research in plant-derived therapeutics possibly due to their relatively lesser toxicity profiles. Flavonoid C-glycosides are one of the plant-derived metabolites gaining increased relevance as antidiabetic agents, but their possible mechanism of action remains largely unknown. This study investigates the antidiabetic potential of flavonoid C-glycosides against PTP1B in silico and in vitro. Of the seven flavonoid C-glycosides docked against the enzyme, three compounds (apigenin, vitexin, and orientin) had the best affinity for the enzyme with a binding score of -7.3 kcal/mol each, relative to -7.4 kcal/mol for the reference standard, ursolic acid. A further probe (in terms of stability, flexibility, and compactness) of the complexes over a molecular dynamics time study of 100 ns for the three compounds suggested orientin as the most outstanding inhibitor of PTP1B owing to its overall -34.47 kcal/mol binding energy score compared to ursolic acid (-19.24 kcal/mol). This observation was in accordance with the in vitro evaluation result, where orientin had a half maximal inhibitory concentration (IC50) of 0.18 mg/ml relative to 0.13 mg/ml for the reference standard. The kinetics of inhibition of PTP1B by orientin was mixed-type with V max and K m values of 0.004 μM/s and 0.515 μM. Put together, the results suggest orientin as a potential PTP1B inhibitor and could therefore be further explored in the management T2DM as a promising therapeutic agent.
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Affiliation(s)
- Athika Rampadarath
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Fatai Oladunni Balogun
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Charlene Pillay
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
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