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Shayo MJ, Samwel B, Shadrack DM, Cassel J, Salvino JM, Montaner LJ, Deogratias G, Tietjen I, Kiruri L, Hilonga S, Innocent E. Drug repositioning identifies salvinorin A and deacetylgedunin (DCG) enriched plant extracts as novel inhibitors of Mpro, RBD-ACE2 and TMPRRS2 proteins. RSC Adv 2024; 14:21203-21212. [PMID: 38966817 PMCID: PMC11223729 DOI: 10.1039/d4ra02593h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/21/2024] [Indexed: 07/06/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) has spread worldwide with severe health, social, and economic repercussions. Although vaccines have significantly reduced the severity of symptoms and deaths, alternative medications derived from natural products (NPs) are vital to further decrease fatalities, especially in regions with low vaccine uptake. When paired with the latest computational developments, NPs, which have been used to cure illnesses and infections for thousands of years, constitute a renewed resource for drug discovery. In the present report, a combination of computational and in vitro methods reveals the repositioning of NPs and identifies salvinorin A and deacetylgedunin (DCG) as having potential anti-SARS-CoV-2 activities. Salvinorin A was found both in silico and in vitro to inhibit both SARS-CoV-2 spike/host ACE2 protein interactions, consistent with blocking viral cell entry, and well as live virus replication. Plant extracts from Azadirachta indica and Cedrela odorata, which contain high levels of DCG, inhibited viral cell replication by targeting the main protease (Mpro) and/or inhibited viral cell entry by blocking the interaction between spike RBD-ACE2 protein at concentrations lower than salvinorin A. Our findings suggest that salvinorin A represent promising chemical starting points where further optimization may result in effective natural product-derived and potent anti-SARS-CoV-2 inhibitors to supplement vaccine efforts.
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Affiliation(s)
- Mariana J Shayo
- Department of Biological and Pre-clinical Studies, Institute of Traditional Medicine, Muhimbili University of Health and Allied Sciences P.O.Box 65001 Dar es Salaam Tanzania
| | - Baraka Samwel
- Department of Natural Products, Institute of Traditional Medicines, Muhimbili University of Health and Allied Sciences P.O.Box 65001 Dar es Salaam Tanzania
| | - Daniel M Shadrack
- Department of Chemistry, Faculty of Natural and Applied Sciences, St. John's University of Tanzania P.O.Box 47 Dodoma Tanzania
- School of Life Science and Bio-engineering, Nelson Mandela African Institute of Science and Technology P.O.Box 447 Arusha Tanzania
| | - Joel Cassel
- The Wistar Institute 3601 Spruce Street Philadelphia PA 19104 USA
| | - Joseph M Salvino
- The Wistar Institute 3601 Spruce Street Philadelphia PA 19104 USA
| | - Luis J Montaner
- The Wistar Institute 3601 Spruce Street Philadelphia PA 19104 USA
| | - Geradius Deogratias
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam P.O.Box 35061 Dar es Salaam Tanzania
| | - Ian Tietjen
- The Wistar Institute 3601 Spruce Street Philadelphia PA 19104 USA
| | - Lucy Kiruri
- Kenyata University, Department of Chemistry P.O.Box 43844-00100 Nairobi Kenya
| | - Samson Hilonga
- Department of Medical Botany, Plant Breeding and Agronomy, Institute of Traditional Medicine, Muhimbili University of Health and Allied Sciences P.O.Box 65001 Dar es Salaam Tanzania
| | - Ester Innocent
- Department of Biological and Pre-clinical Studies, Institute of Traditional Medicine, Muhimbili University of Health and Allied Sciences P.O.Box 65001 Dar es Salaam Tanzania
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2
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Hu YX, Fei JW, Bie LH, Gao J. Simulation of the ligand-leaving process of the human heat shock protein. Phys Chem Chem Phys 2023; 25:28465-28472. [PMID: 37846475 DOI: 10.1039/d3cp03372d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The human heat shock protein plays a critical role in various diseases and is an important target for pharmacological modulation. Simulation of conformational changes and free energy profiles of the human heat shock protein derived by the ligand-leaving process is a challenging issue. In this work, steered molecular dynamics simulation was adopted to simulate the ligand-leaving process. Two composite systems of heat shock protein NHSP90 and small molecules 6FJ and 6G7 are selected as research objects. The free energy during the leaving of ligand small molecules is calculated using conventional molecular dynamics simulation, steered molecular dynamics simulation (SMD), and the umbrella sampling method. We found that the a slower pulling velocity (0.001 nm ns-1) will result in 2.19 kcal mol-1, and the umbrella sampling method gives a value of 3.26 kcal mol-1 for the free energy difference for the two systems, which reasonably agrees with experimental results. A faster-pulling velocity (0.01 nm ns-1) leads to a large overestimation of free energy. At the same time, the conformational analysis indicated that the faster pulling velocity may lead to the conformational change of NHSP90, which was proved to be false by the slower pulling velocity and the umbrella sampling method.
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Affiliation(s)
- Yi-Xiao Hu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Jun-Wen Fei
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Li-Hua Bie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
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3
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Singh H, Almaazmi SY, Dutta T, Keyzers RA, Blatch GL. In silico identification of modulators of J domain protein-Hsp70 interactions in Plasmodium falciparum: a drug repurposing strategy against malaria. Front Mol Biosci 2023; 10:1158912. [PMID: 37621993 PMCID: PMC10445141 DOI: 10.3389/fmolb.2023.1158912] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Plasmodium falciparum is a unicellular, intracellular protozoan parasite, and the causative agent of malaria in humans, a deadly vector borne infectious disease. A key phase of malaria pathology, is the invasion of human erythrocytes, resulting in drastic remodeling by exported parasite proteins, including molecular chaperones and co-chaperones. The survival of the parasite within the human host is mediated by P. falciparum heat shock protein 70s (PfHsp70s) and J domain proteins (PfJDPs), functioning as chaperones-co-chaperones partnerships. Two complexes have been shown to be important for survival and pathology of the malaria parasite: PfHsp70-x-PFE0055c (exported); and PfHsp70-2-PfSec63 (endoplasmic reticulum). Virtual screening was conducted on the drug repurposing library, the Pandemic Response Box, to identify small-molecules that could specifically disrupt these chaperone complexes. Five top ranked compounds possessing preferential binding affinity for the malarial chaperone system compared to the human system, were identified; three top PfHsp70-PfJDP binders, MBX 1641, zoliflodacin and itraconazole; and two top J domain binders, ezetimibe and a benzo-diazepinone. These compounds were validated by repeat molecular dockings and molecular dynamics simulation, resulting in all the compounds, except for MBX 1461, being confirmed to bind preferentially to the malarial chaperone system. A detailed contact analysis of the PfHsp70-PfJDP binders identified two different types of modulators, those that potentially inhibit complex formation (MBX 1461), and those that potentially stabilize the complex (zoliflodacin and itraconazole). These data suggested that zoliflodacin and itraconazole are potential novel modulators specific to the malarial system. A detailed contact analysis of the J domain binders (ezetimibe and the benzo-diazepinone), revealed that they bound with not only greater affinity but also a better pose to the malarial J domain compared to that of the human system. These data suggested that ezetimibe and the benzo-diazepinone are potential specific inhibitors of the malarial chaperone system. Both itraconazole and ezetimibe are FDA-approved drugs, possess anti-malarial activity and have recently been repurposed for the treatment of cancer. This is the first time that such drug-like compounds have been identified as potential modulators of PfHsp70-PfJDP complexes, and they represent novel candidates for validation and development into anti-malarial drugs.
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Affiliation(s)
- Harpreet Singh
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, India
| | - Shaikha Y. Almaazmi
- Biomedical Research and Drug Discovery Research Group, Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
| | - Tanima Dutta
- Department of Diagnostic Genomics, Path West Nedlands, QEII Medical Centre, Nedlands, WA, Australia
| | - Robert A. Keyzers
- Centre for Biodiscovery & School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Gregory L. Blatch
- Biomedical Research and Drug Discovery Research Group, Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
- Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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Vuai SAH, Ogedjo MM, Isaac O, Sahini MG, Swai HS, Shadrack DM. Relaxed complex scheme and molecular dynamics simulation suggests small molecule inhibitor of human TMPRSS2 for combating COVID-19. J Biomol Struct Dyn 2022; 40:13925-13935. [PMID: 34751094 DOI: 10.1080/07391102.2021.1997817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Said A H Vuai
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma, Dodoma, Tanzania
| | - Marcelina M Ogedjo
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma, Dodoma, Tanzania
| | - Onoka Isaac
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma, Dodoma, Tanzania
| | - Mtabazi G Sahini
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma, Dodoma, Tanzania
| | - Hulda S Swai
- School of Life Sciences and Bioengineering, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Daniel M Shadrack
- Department of Chemistry, Faculty of Natural and Applied Sciences, St. John's University of Tanzania, Dodoma, Tanzania
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5
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Stachowski TR, Fischer M. Large-Scale Ligand Perturbations of the Protein Conformational Landscape Reveal State-Specific Interaction Hotspots. J Med Chem 2022; 65:13692-13704. [PMID: 35970514 PMCID: PMC9619398 DOI: 10.1021/acs.jmedchem.2c00708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Protein flexibility is important for ligand binding but
often ignored
in drug design. Considering proteins as ensembles rather than static
snapshots creates opportunities to target dynamic proteins that lack
FDA-approved drugs, such as the human chaperone, heat shock protein
90 (Hsp90). Hsp90α accommodates ligands with a dynamic lid domain,
yet no comprehensive analysis relating lid conformations to ligand
properties is available. To date, ∼300 ligand-bound Hsp90α
crystal structures are deposited in the Protein Data Bank, which enables
us to consider ligand binding as a perturbation of the protein conformational
landscape. By estimating binding site volumes, we classified structures
into distinct major and minor lid conformations. Supported by retrospective
docking, each conformation creates unique hotspots that bind chemically
distinguishable ligands. Clustering revealed insightful exceptions
and the impact of crystal packing. Overall, Hsp90α’s
plasticity provides a cautionary tale of overinterpreting individual
crystal structures and motivates an ensemble-based view of drug design.
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Affiliation(s)
- Timothy R Stachowski
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Marcus Fischer
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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Belousov R, Hassanali A, Roldán É. Statistical physics of inhomogeneous transport: Unification of diffusion laws and inference from first-passage statistics. Phys Rev E 2022; 106:014103. [PMID: 35974517 DOI: 10.1103/physreve.106.014103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Characterization of composite materials, whose properties vary in space over microscopic scales, has become a problem of broad interdisciplinary interest. In particular, estimation of the inhomogeneous transport coefficients, e.g., the diffusion coefficient or the heat conductivity, which shape important processes in biology and engineering, is a challenging task. The analysis of such systems is further complicated because two alternative formulations of the inhomogeneous transport equations exist in the literature-the Smoluchowski and Fokker-Planck equations, which are also related to the so-called Ito-Stratonovich dilemma. Using the theory of statistical physics, we show that the two formulations, usually regarded as distinct models, are physically equivalent. From this result we develop efficient estimates for the transverse space-dependent diffusion coefficient in fluids near a phase boundary. Our method requires only measurements of escape probabilities and mean exit times of molecules leaving a narrow spatial region. We test our estimates in three case studies: (i) a Langevin model of a Büttikker-Landauer ratchet; atomistic molecular-dynamics simulations of liquid-water molecules in contact with (ii) vapor, and (iii) soap (surfactant) film which has promising applications in physical chemistry. Our analysis reveals that near the surfactant monolayer the mobility of water molecules is slowed down almost twice with respect to the bulk liquid. Moreover, the diffusion coefficient of water correlates with the transition from hydrophilic to hydrophobic parts of the film.
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Affiliation(s)
- Roman Belousov
- ICTP-The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Ali Hassanali
- ICTP-The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Édgar Roldán
- ICTP-The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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7
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Heat Shock Protein 90 (HSP90) Inhibitors as Anticancer Medicines: A Review on the Computer-Aided Drug Discovery Approaches over the Past Five Years. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:2147763. [PMID: 35685897 PMCID: PMC9173959 DOI: 10.1155/2022/2147763] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 05/08/2022] [Accepted: 05/19/2022] [Indexed: 12/24/2022]
Abstract
Cancer is a disease caused by the uncontrolled, abnormal growth of cells in different anatomic sites. In 2018, it was predicted that the worldwide cancer burden would rise to 18.1 million new cases and 9.6 million deaths. Anticancer compounds, often known as chemotherapeutic medicines, have gained much interest in recent cancer research. These medicines work through various biological processes in targeting cells at various stages of the cell's life cycle. One of the most significant roadblocks to developing anticancer drugs is that traditional chemotherapy affects normal cells and cancer cells, resulting in substantial side effects. Recently, advancements in new drug development methodologies and the prediction of the targeted interatomic and intermolecular ligand interaction sites have been beneficial. This has prompted further research into developing and discovering novel chemical species as preferred therapeutic compounds against specific cancer types. Identifying new drug molecules with high selectivity and specificity for cancer is a prerequisite in the treatment and management of the disease. The overexpression of HSP90 occurs in patients with cancer, and the HSP90 triggers unstable harmful kinase functions, which enhance carcinogenesis. Therefore, the development of potent HSP90 inhibitors with high selectivity and specificity becomes very imperative. The activities of HSP90 as chaperones and cochaperones are complex due to the conformational dynamism, and this could be one of the reasons why no HSP90 drugs have made it beyond the clinical trials. Nevertheless, HSP90 modulations appear to be preferred due to the competitive inhibition of the targeted N-terminal adenosine triphosphate pocket. This study, therefore, presents an overview of the various computational models implored in the development of HSP90 inhibitors as anticancer medicines. We hereby suggest an extensive investigation of advanced computational modelling of the three different domains of HSP90 for potent, effective inhibitor design with minimal off-target effects.
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8
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Stofberg ML, Caillet C, de Villiers M, Zininga T. Inhibitors of the Plasmodium falciparum Hsp90 towards Selective Antimalarial Drug Design: The Past, Present and Future. Cells 2021; 10:2849. [PMID: 34831072 PMCID: PMC8616389 DOI: 10.3390/cells10112849] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/12/2022] Open
Abstract
Malaria is still one of the major killer parasitic diseases in tropical settings, posing a public health threat. The development of antimalarial drug resistance is reversing the gains made in attempts to control the disease. The parasite leads a complex life cycle that has adapted to outwit almost all known antimalarial drugs to date, including the first line of treatment, artesunate. There is a high unmet need to develop new strategies and identify novel therapeutics to reverse antimalarial drug resistance development. Among the strategies, here we focus and discuss the merits of the development of antimalarials targeting the Heat shock protein 90 (Hsp90) due to the central role it plays in protein quality control.
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Affiliation(s)
| | | | | | - Tawanda Zininga
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa; (M.L.S.); (C.C.); (M.d.V.)
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9
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Ogedjo M, Onoka I, Sahini M, Shadrack DM. Accommodating receptor flexibility and free energy calculation to reduce false positive binders in the discovery of natural products blockers of SARS-COV-2 spike RBD-ACE2 interface. Biochem Biophys Rep 2021; 27:101024. [PMID: 34056140 PMCID: PMC8148615 DOI: 10.1016/j.bbrep.2021.101024] [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: 02/15/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 11/28/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), which causes coronavirus disease-19 (COVID-19) has caused more than 2 million deaths around the globe. The high transmissibility rate of the disease is related to the strong interaction between the virus spike receptor-binding domain (RBD) and the human angiotensin-converting enzyme 2 (ACE2) as documented in several reports. In this study, using state-of-the-art computational methods, natural products were screened and their molecular mechanism to disrupt spike RBD-ACE2 recognition was evaluated. There is the sensitivity of results to receptor ensemble docking calculations. Binding free energy and MD simulation are important tools to evaluate the thermodynamics of binding stability and the capacity of top hits to disrupt RBD-ACE2 recognition. The free energy profiles provide a slight decrease in binding affinity of the virus-receptor interaction. Three flavonoids parvisoflavone B (3), alpinumisoflavone (5) and norisojamicin (2) were effective in blocking the viral entry by binding strongly at the spike RBD-ACE2 interface with the inhibition constant of 0.56, 0.78 and 0.93 μM, respectively. The same compounds demonstrated similar effect on free ACE2 protein. Compound (2), also demonstrated ability to bind strongly on free spike RBD. Well-tempered metadynamics established that parvisoflavone B (3) works by binding to three sites namely interface α, β and loop thereby inhibiting viral cell entry. Owing to their desirable pharmacokinetic properties, the presented top hit natural products are suggested for further SARS-COV-2 molecular targets and subsequent in vitro and in vivo evaluations.
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Affiliation(s)
- Marcelina Ogedjo
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma, P.O.Box 338, Dodoma, Tanzania
| | - Isaac Onoka
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma, P.O.Box 338, Dodoma, Tanzania
| | - Mtabazi Sahini
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma, P.O.Box 338, Dodoma, Tanzania
| | - Daniel M. Shadrack
- Department of Chemistry, Faculty of Natural and Applied Sciences, St. John's University of Tanzania, P.O.Box 47, Dodoma, Tanzania
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10
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Shadrack DM, Vuai SAH, Sahini MG, Onoka I. In silico study of the inhibition of SARS-COV-2 viral cell entry by neem tree extracts. RSC Adv 2021; 11:26524-26533. [PMID: 35480004 PMCID: PMC9037307 DOI: 10.1039/d1ra04197e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/03/2021] [Indexed: 12/13/2022] Open
Abstract
The outbreak of COVID-19, caused by SARS-COV-2, is responsible for higher mortality and morbidity rates across the globe. Until now, there is no specific treatment of the disease and hospitalized patients are treated according to the symptoms they develop. Efforts to identify drugs and/or vaccines are ongoing processes. Natural products have shown great promise in the treatment of many viral related diseases. In this work, using in silico methods, bioactive compounds from the neem tree were investigated for their ability to block viral cell entry as spike RBD-ACE2 inhibitors. Azadirachtin H, quentin and margocin were identified as potential compounds that demonstrated viral cell entry inhibition properties. The structural re-orientation of azadirachtin H was observed as the mechanism for viral cell entry inhibition. These compounds possessed good pharmacodynamic properties. The proposed molecules can serve as a starting point towards developing effective anti-SARS-COV-2 drugs targeting the inhibition of viral cell entry upon further in vitro and in vivo validation. The outbreak of COVID-19, caused by SARS-COV-2, is responsible for higher mortality and morbidity rates across the globe.![]()
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Affiliation(s)
- Daniel M Shadrack
- Department of Chemistry, Faculty of Natural and Applied Sciences, St John's University of Tanzania Dodoma P. O. Box 47 +255 713 696 089
| | - Said A H Vuai
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma Dodoma P. O. Box 338 Tanzania
| | - Mtabazi G Sahini
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma Dodoma P. O. Box 338 Tanzania
| | - Isaac Onoka
- Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma Dodoma P. O. Box 338 Tanzania
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11
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Luteolin: a blocker of SARS-CoV-2 cell entry based on relaxed complex scheme, molecular dynamics simulation, and metadynamics. J Mol Model 2021; 27:221. [PMID: 34236507 PMCID: PMC8264176 DOI: 10.1007/s00894-021-04833-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022]
Abstract
Natural products have served human life as medications for centuries. During the outbreak of COVID-19, a number of naturally derived compounds and extracts have been tested or used as potential remedies against COVID-19. Tetradenia riparia extract is one of the plant extracts that have been deployed and claimed to manage and control COVID-19 by some communities in Tanzania and other African countries. The active compounds isolated from T. riparia are known to possess various biological properties including antimalarial and antiviral. However, the underlying mechanism of the active compounds against SARS-CoV-2 remains unknown. Results in the present work have been interpreted from the view point of computational methods including molecular dynamics, free energy methods, and metadynamics to establish the related mechanism of action. Among the constituents of T. riparia studied, luteolin inhibited viral cell entry and was thermodynamically stable. The title compound exhibit residence time and unbinding kinetics of 68.86 ms and 0.014 /ms, respectively. The findings suggest that luteolin could be potent blocker of SARS-CoV-2 cell entry. The study shades lights towards identification of bioactive constituents from T. riparia against COVID-19, and thus bioassay can be carried out to further validate such observations.
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12
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Begum S, Shadrack DM, Joseph FM, Ndensendo VMK. Molecular dynamics simulation of bioactive compounds of Withania somnifera leaf extract as DNA gyrase inhibitor. J Biomol Struct Dyn 2021; 40:9279-9286. [PMID: 34018468 DOI: 10.1080/07391102.2021.1927191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Medicinal plants have served humans as medicine for centuries. Withania somnifera (L.) (Ashwagandha) leaf extract is traditionally used in managing and treating bacterial infections. A combination of experimental and computational methods was used to investigate the related antibacterial mechanism. Leaf extract showed strong antibacterial activity against S. aureus. Moreover, molecular docking established that withanolide C, a compound obtained from methanolic leaf extract binded strongly to DNA gyrase enzyme. Molecular dynamics simulation and molecular mechanics Poisson-Boltzmann surface area binding free energy suggested withanolide C to be stable at the active site of DNA gyrase B. The compound binded in a different fashion as compared to chlorobiocin a known DNA gyrase inhibitor. Present finding suggests that the antibacterial activity of W. somnifera is due to inhibition of DNA gyrase by withanolide C. This finding serves as the basis for development of novel antimicrobial agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sartaz Begum
- School of Pharmacy, St. John's University of Tanzania, Dodoma, Tanzania
| | - Daniel M Shadrack
- Department of Chemistry, Faculty of Natural and Applied Sciences, St. John's University of Tanzania, Dodoma, Tanzania
| | - Ferister M Joseph
- School of Pharmacy, St. John's University of Tanzania, Dodoma, Tanzania
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