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S S, V S, I JM, P VM, P LK, Nair AS, R SP, Oommen OV. In silico screening of the phytochemicals present in Clitoria ternatea L. as the inhibitors of snake venom phospholipase A 2 (PLA 2). J Biomol Struct Dyn 2023; 41:7874-7883. [PMID: 36153001 DOI: 10.1080/07391102.2022.2126889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 09/15/2022] [Indexed: 10/14/2022]
Abstract
Millions of people suffer from snake bite envenomation, and its management is a challenge, even today. Medicinal plants have attracted the researcher's attention for their outstanding advantages in treating many diseases, including snake venom poisoning. Clitoria ternatea L, is a plant popularly known for its various pharmacological effects especially, anti-snake venom property. However, the molecular mechanism behind this is poorly understood. It is reported that snake venom PLA2 is an extensively studied toxic factor. This study is meant to screen the compound's capability to act as inhibitors of the Daboia russelli snake venom PLA2 through molecular docking and dynamics studies. Our results show that among the 27 compounds taken for the study, only Kaempferol showed good interaction profile with the conserved catalytic active site residues, His48 and Asp49. The pharmacophore features of the compound also demonstrate its exact fitting at the binding pocket. Further RMSD, RMSF, Rg, and hydrogen bond analysis confirmed the stable binding of Kaempferol with PLA2 through molecular dynamic simulations for 100 ns. In addition, the MM/PBSA binding free energy calculation of the complex was also affirming the docking results. The binding free energy (BFE) of Kaempferolis better than the reference compound. ADME and Lipinski's rule of five reveals its drug like properties.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suveena S
- Centre for Venom Informatics, Department of Computational Biology & Bioinformatics, University of Kerala, Trivandrum, Kerala, India
| | - Saraswathy V
- Centre for Venom Informatics, Department of Computational Biology & Bioinformatics, University of Kerala, Trivandrum, Kerala, India
| | - Junaida M I
- Centre for Venom Informatics, Department of Computational Biology & Bioinformatics, University of Kerala, Trivandrum, Kerala, India
| | - Vinod M P
- Centre for Venom Informatics, Department of Computational Biology & Bioinformatics, University of Kerala, Trivandrum, Kerala, India
| | - Laladhas K P
- Department of Zoology, St.Stephen's College, Kollam, Kerala, India
| | - Achuthsankar S Nair
- Centre for Venom Informatics, Department of Computational Biology & Bioinformatics, University of Kerala, Trivandrum, Kerala, India
| | - Sudhakaran P R
- Centre for Venom Informatics, Department of Computational Biology & Bioinformatics, University of Kerala, Trivandrum, Kerala, India
| | - Oommen V Oommen
- Centre for Venom Informatics, Department of Computational Biology & Bioinformatics, University of Kerala, Trivandrum, Kerala, India
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Mahmud S, Parves MR, Riza YM, Sujon KM, Ray S, Tithi FA, Zaoti ZF, Alam S, Absar N. Exploring the potent inhibitors and binding modes of phospholipase A2 through in silico investigation. J Biomol Struct Dyn 2019; 38:4221-4231. [PMID: 31607222 DOI: 10.1080/07391102.2019.1680440] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Snake venom of Naja naja comprises of several types of enzymes, and among them, water-soluble proteolytic enzyme, phospholipase A2 (PLA2), is noteworthy for its numerous adverse effects, such as cytotoxicity, cardiotoxicity, hemolytic, anti-coagulant, and hypotensive effects, including being highly potent as a neurotoxin. Limited anti-venom therapy (with their lower efficacy) has attracted considerable pharmacological interest to develop potent inhibitors of PLA2. Thus, 34 experimentally proven and diverse synthetic inhibitors of PLA2 were screened primarily on the basis of Glide extra precision docking and MM-GBSA rescoring function. Then, ten potential hits were subjected to induced fit docking, in which top three potential inhibitors were considered, and those were found to interact with Ca2+, disulfide binding site, and phosphatidylcholine activation sites, thereby, possibly disrupting the catalytic activity of Ca2+ as well as the inflammatory functions of PLA2. These compounds showed positive remarks on various physiochemical properties and pharmacologically relevant descriptors. Gap energy and thermodynamic properties were investigated by employing density functional theory for all compounds to understand their chemical reactivity and thermodynamic stability. Molecular dynamics simulation was performed for 100 ns in order to evaluate the stability and binding modes of docked complexes, and the energy of binding was calculated through MM-PBSA analysis. On the whole, the proposed compounds could be used for targeted inhibition. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, Molecular Biology and Protein Science Laboratory, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Rimon Parves
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | - Yasir Mohamed Riza
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | - Khaled Mahmud Sujon
- Department of Genetic Engineering and Biotechnology, Molecular Biology and Protein Science Laboratory, University of Rajshahi, Rajshahi, Bangladesh
| | - Suvendu Ray
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | - Fahmida Alam Tithi
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | | | - Sanjida Alam
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
| | - N Absar
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Chittagong, Bangladesh
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Molecular docking and dynamic studies of crepiside E beta glucopyranoside as an inhibitor of snake venom PLA2. J Mol Model 2019; 25:88. [PMID: 30847632 DOI: 10.1007/s00894-019-3954-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 01/29/2019] [Indexed: 02/07/2023]
Abstract
Alternative treatments from plant-derived small molecules for neutralizing the venom lethality in snake envenomation are prevalent now. Elephantopus scaber, a tropical plant species has been recognized for its various pharmacological activities and especially anti-snake venom property; however, the molecular basis for this property is not understood. It is reported that snake venom PLA2 is a toxic factor with pharmacological effects independent of their catalytic activity. Here we report the inhibition of catalytic property of Cobra and Viper (group I and group II) snake venom PLA2 by the phytocompounds from E. scaber through molecular docking and dynamics studies. Initially, Lipinski's rule, ADMET, and molecular docking studies were carried out. Our results show that among 124 phytocompounds, crepiside E (deacylcynaropicrin-3' beta-glucopyranoside) has shown interactions with the conserved catalytic active site residues, His 48 and Asp 49, in both the PLA2s. Further, molecular dynamic simulations for 60 ns confirmed the stability of crepiside E in the active site of PLA2s and were found to be stable throughout the simulation. In order to understand the drug-likeness of crepiside E, pIC50 and MMGBSA scores were correlated by performing a linear regression analysis. Crepiside E was found to have similar chemical features to that of doxycycline, a known PLA2 inhibitor as indicated by a similarity score of 64.15%. Hence, it is concluded that crepiside E beta glucopyranoside present in Elephantopus scaber contributes to neutralizing the snake venom.
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Ojeda PG, Ramírez D, Alzate-Morales J, Caballero J, Kaas Q, González W. Computational Studies of Snake Venom Toxins. Toxins (Basel) 2017; 10:E8. [PMID: 29271884 PMCID: PMC5793095 DOI: 10.3390/toxins10010008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/09/2017] [Accepted: 12/18/2017] [Indexed: 12/17/2022] Open
Abstract
Most snake venom toxins are proteins, and participate to envenomation through a diverse array of bioactivities, such as bleeding, inflammation, and pain, cytotoxic, cardiotoxic or neurotoxic effects. The venom of a single snake species contains hundreds of toxins, and the venoms of the 725 species of venomous snakes represent a large pool of potentially bioactive proteins. Despite considerable discovery efforts, most of the snake venom toxins are still uncharacterized. Modern bioinformatics tools have been recently developed to mine snake venoms, helping focus experimental research on the most potentially interesting toxins. Some computational techniques predict toxin molecular targets, and the binding mode to these targets. This review gives an overview of current knowledge on the ~2200 sequences, and more than 400 three-dimensional structures of snake toxins deposited in public repositories, as well as of molecular modeling studies of the interaction between these toxins and their molecular targets. We also describe how modern bioinformatics have been used to study the snake venom protein phospholipase A2, the small basic myotoxin Crotamine, and the three-finger peptide Mambalgin.
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Affiliation(s)
- Paola G Ojeda
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomedicas, Universidad Autonoma de Chile, 3460000 Talca, Chile.
| | - David Ramírez
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomedicas, Universidad Autonoma de Chile, 3460000 Talca, Chile.
| | - Jans Alzate-Morales
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
| | - Julio Caballero
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Wendy González
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, 3460000 Talca, Chile.
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Lewin M, Samuel S, Merkel J, Bickler P. Varespladib (LY315920) Appears to Be a Potent, Broad-Spectrum, Inhibitor of Snake Venom Phospholipase A2 and a Possible Pre-Referral Treatment for Envenomation. Toxins (Basel) 2016; 8:toxins8090248. [PMID: 27571102 PMCID: PMC5037474 DOI: 10.3390/toxins8090248] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/11/2016] [Accepted: 08/15/2016] [Indexed: 01/07/2023] Open
Abstract
Snakebite remains a neglected medical problem of the developing world with up to 125,000 deaths each year despite more than a century of calls to improve snakebite prevention and care. An estimated 75% of fatalities from snakebite occur outside the hospital setting. Because phospholipase A2 (PLA2) activity is an important component of venom toxicity, we sought candidate PLA2 inhibitors by directly testing drugs. Surprisingly, varespladib and its orally bioavailable prodrug, methyl-varespladib showed high-level secretory PLA2 (sPLA2) inhibition at nanomolar and picomolar concentrations against 28 medically important snake venoms from six continents. In vivo proof-of-concept studies with varespladib had striking survival benefit against lethal doses of Micrurus fulvius and Vipera berus venom, and suppressed venom-induced sPLA2 activity in rats challenged with 100% lethal doses of M. fulvius venom. Rapid development and deployment of a broad-spectrum PLA2 inhibitor alone or in combination with other small molecule inhibitors of snake toxins (e.g., metalloproteases) could fill the critical therapeutic gap spanning pre-referral and hospital setting. Lower barriers for clinical testing of safety tested, repurposed small molecule therapeutics are a potentially economical and effective path forward to fill the pre-referral gap in the setting of snakebite.
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Affiliation(s)
- Matthew Lewin
- Research and Development, Ophirex, Inc., Corte Madera, CA 94925, USA.
- Center for Exploration and Travel Health, California Academy of Sciences, San Francisco, CA 94118, USA.
| | - Stephen Samuel
- General Medicine, Queen Elizabeth Hospital, King's Lynn, Norfolk PE30 4ET, UK.
| | - Janie Merkel
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA.
| | - Philip Bickler
- Anesthesia and Perioperative Care, University of California, San Francisco, CA 94143, USA.
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Sivaramakrishnan V, Ilamathi M, Girish KS, Kemparaju K, Rangappa KS, Dhananjaya BL. Viper venom hyaluronidase and its potential inhibitor analysis: a multipronged computational investigation. J Biomol Struct Dyn 2016; 35:1979-1989. [PMID: 27334983 DOI: 10.1080/07391102.2016.1203820] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Viper venom hyaluronidase (VV-HYA) inhibitors have long been used as therapeutic agents for arresting the local and systemic effects caused during its envenomation. Henceforth, to understand its structural features and also to identify the best potential inhibitor against it the present computational study was undertaken. Structure-based homology modeling of VV-HYA followed by its docking and free energy-based ranking analysis of ligand, the MD simulations of the lead complex was also performed. The sequence analysis and homology modeling of VV-HYA revealed a distorted (β/α)8 folding as in the case of hydrolases family of proteins. Molecular docking of the resultant 3D structure of VV-HYA with known inhibitors (compounds 1-25) revealed the importance of molecular recognition of hotspot residues (Tyr 75, Arg 288, and Trp 321) other than that of the active site residues. It also revealed that Trp 321 of VV-HYA is highly important for mediating π-π interactions with ligands. In addition, the molecular docking and comparative free energy binding analysis was investigated for the VV-HYA inhibitors (compounds 1-25). Both molecular docking and relative free energy binding analysis clearly confirmed the identification of sodium chromoglycate (compound 1) as the best potential inhibitor against VV-HYA. Molecular dynamics simulations additionally confirmed the stability of their binding interactions. Further, the information obtained from this work is believed to serve as an impetus for future rational designing of new novel VV-HYA inhibitors with improved activity and selectivity.
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Affiliation(s)
- V Sivaramakrishnan
- a Cardiomyocyte Toxicity and Oncology Research Lab, Department of Bioinformatics, School of Chemical and Biotechnology , SASTRA University , Thirumalaisamudram, Thanjavur 613402 , Tamil Nadu , India
| | - M Ilamathi
- a Cardiomyocyte Toxicity and Oncology Research Lab, Department of Bioinformatics, School of Chemical and Biotechnology , SASTRA University , Thirumalaisamudram, Thanjavur 613402 , Tamil Nadu , India
| | - K S Girish
- b Department of Studies in Biochemistry , University of Mysore , Mysore 570006 , Karnataka , India.,c Department of Biochemistry , Tumkur University , Tumkur , Karnataka , India
| | - K Kemparaju
- b Department of Studies in Biochemistry , University of Mysore , Mysore 570006 , Karnataka , India
| | - K S Rangappa
- d Department of Chemistry , University of Mysore , Mysore 570006 , India
| | - Bhadrapura Lakkappa Dhananjaya
- a Cardiomyocyte Toxicity and Oncology Research Lab, Department of Bioinformatics, School of Chemical and Biotechnology , SASTRA University , Thirumalaisamudram, Thanjavur 613402 , Tamil Nadu , India.,e Toxinology/Toxicology and Drug Discovery Unit, Center for Emerging Technologies , Jain University , Jakkasandra Post, Ramanagara 562112 , India
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Dhananjaya BL, Sudarshan S, Dongol Y, More SS. The standard aqueous stem bark extract of Mangifera indica L. inhibits toxic PLA2 - NN-XIb-PLA2 of Indian cobra venom. Saudi Pharm J 2016; 24:371-8. [PMID: 27275129 PMCID: PMC4881193 DOI: 10.1016/j.jsps.2016.04.026] [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] [Indexed: 11/30/2022] Open
Abstract
The aqueous extract of Mangifera indica is known to possess diverse medicinal properties, which also includes anti-snake venom activities. However, its inhibitory potency and mechanism of action on multi-toxic snake venom phospholipases A2s are still unknown. Therefore, the objective of this study was to evaluate the modulatory effect of standard aqueous bark extract of M. indica on NN-XIb-PLA2 of Indian cobra venom. The in vitro sPLA2, in situ hemolytic and in vivo edema inhibition effect were carried out as described. Also the effect of substrate and calcium concentration was carried out. M. indica extract dose dependently inhibited the GIA sPLA2 (NN-XIb-PLA2) activity with an IC50 value of 7.6 μg/ml. M. indica extract effectively inhibited the indirect hemolytic activity up to 98% at ∼40 μg/ml concentration. Further, M. indica extract (0–50 μg/ml) inhibited the edema formed in a dose dependent manner. When examined as a function of increased substrate and calcium concentration, there was no relieve of inhibitory effect of M. indica extract on the NN-XIb-PLA2. Further, the inhibition was irreversible as evident from binding studies. The in vitro inhibition is well correlated with in situ and in vivo edema inhibiting activities of M. indica. As the inhibition is independent of substrate and calcium and was irreversible, it can be concluded that M. indica extract mode of inhibition could be due to direct interaction of components present in the extract with the PLA2 enzyme. The aqueous extract of M. indica effectively inhibits svPLA2 enzymatic and its associated toxic activities, which substantiate their anti-snake venom properties. Further in-depth studies on the role and mechanism of the principal constituents present in the extract, responsible for the anti-PLA2 activity will be interesting to develop them into potent antisnake component and also as an anti-inflammatory agent.
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Affiliation(s)
- Bhadrapura Lakkappa Dhananjaya
- Venom Research Unit, Adichunchanagiri Biotechnology and Cancer Research Institute (ABCRI), Balagangadharanatha Nagara, Mandya District, Karnataka 571 448, India; Toxinology/Toxicology and Drug Discovery Unit, Center for Emerging Technologies, Jain Global Campus, Jain University, Kanakapura Taluk, Ramanagara 562112, Karnataka, India
| | - Shivalingaiah Sudarshan
- Venom Research Unit, Adichunchanagiri Biotechnology and Cancer Research Institute (ABCRI), Balagangadharanatha Nagara, Mandya District, Karnataka 571 448, India
| | - Yashad Dongol
- Department of Biochemistry, KIST Medical College, Lalitpur, Kathmandu, Nepal
| | - Sunil S More
- School of Basic and Applied Sciences, Dayananda Sagar University, K.S. Layout, SM Hills, Bangalore 560078, India
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