Physicochemical characterization and functional analysis of some snake venom toxin proteins and related non-toxin proteins of other chordates

Panda, Subhamay; Chandra, Goutam

doi:10.6026/97320630008891

Cited by 66 publications

(41 citation statements)

References 17 publications

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“…For the translocation of BAX to mitochondria, a mitochondrial addressing signal of N-terminal Hα1 is believed to be necessary [29]. Recent bioinformatical research methods were very helpful for the discovery process of new biologically and biomedically important protein molecules [30][31][32][33][34][35][36][37][38][39]. Therefore, varied structural forms of BAX molecules in the different organisms (e.g., Chinese liver fluke) must be identified for bio-medical interventions.…”

Section: Resultsmentioning

confidence: 99%

The Biophysical Characteristics and Structural Exploration of Programmed Cell Death Regulator B-Cell Lymphoma 2-Associated X Protein of Chinese Liver Fluke (Clonorchis Sinensis)

Panda¹,

Prasad²,

Bag³

2017

Asian J Pharm Clin Res

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Objective: The balance between deaths and cellular life is regulated by B-cell lymphoma 2 (BCL-2)-associated X protein (BAX) an important proapoptotic components of BCL-2 family. With this initial point, the aim of this study was to determine a comparative composite based structure of BAX of Chinese liver fluke and different structural analysis. Methods:Protein amino acid of BAX of Chinese liver fluke mined from National Centre for Biotechnology Information (http://ncbi.nlm.nih.gov). Molecular model of BAX of Chinese liver fluke protein was generated by the comparative composite modeling tool Iterative Threading ASSEmbly Refinement suite. Afterward, I-TASSER generated molecular model was subjected to further structural improvements by energy minimization step. Distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, and hydrophobicity molecular surface analysis was performed with the help of bioinformatical tools.Results: Analysis of Ramachandran plot created by PROCHECK tool is a consensus standard for validation purpose of protein structural modeling. Altogether 97.8% of the residues were detected in allowed and favored regions, which in turn validate the quality of generated protein structural model. Total negatively and positively charged residues within the BAX of Chinese liver fluke were 23 and 20, respectively. Chimera package-guided hydrophobicity molecular surface analysis illustrates that molecule specific hydrophobicity surface is exclusive to BAX protein molecule. Conclusion:Within the scope of this scientific investigation, we have successfully utilized molecular modeling approach to suggest the first molecular three-dimensional model structure of BAX of Chinese liver fluke. The synchronous balance between cellular deaths and cellular life is keeping up by BAX, an important pro-apoptotic family member of BCL-2 family. Consequently, it would be an exciting approach to resolve its structural characterization and molecular structure to propose mode of mechanism action.

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Section: Resultsmentioning

confidence: 99%

The Biophysical Characteristics and Structural Exploration of Programmed Cell Death Regulator B-Cell Lymphoma 2-Associated X Protein of Chinese Liver Fluke (Clonorchis Sinensis)

Panda¹,

Prasad²,

Bag³

2017

Asian J Pharm Clin Res

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“…It assesses analytically the volume as well as the area of each cavity and pocket, both in molecular surface (MS, Connolly's surface) and solvent accessible surface (SA, Richards' surface). It also measures the number of mouth openings, circumference of mouth lips, and area of the openings, in both SA and MS surfaces for each pocket [18]. …”

Section: Methodsmentioning

confidence: 99%

An insight into the lignin peroxidase of Macrophomina phaseolina

Akbar

Habib²,

Chowdhury³

et al. 2013

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Macrophomina phaseolina is one of the deadliest necrotrophic fungal pathogens that infect more than 500 plant species including major food, fiber, and oil crops all throughout the globe. It secretes a cocktail of ligninolytic enzymes along with other hydrolytic enzymes for degrading the woody lignocellulosic plant cell wall and penetrating into the host tissue. Among them, lignin peroxidase has been reported only in Phanerochaete chrysosporium so far. But interestingly, a recent study has revealed a second occurrence of lignin peroxidase in M. phaseolina. However, lignin peroxidases are of much significance biotechnologically because of their potential applications in bio-remedial waste treatment and in catalyzing difficult chemical transformations. Besides, this enzyme also possesses agricultural and environmental importance on account of their role in lignin biodegradation. In the present work, different properties of the lignin peroxidase of M. phaseolina along with predicting the 3-D structure and its active sites were investigated by the use of various computational tools. The data from this study will pave the way for more detailed exploration of this enzyme in wet lab and thereby facilitating the strategies to be designed against such deadly weapons of Macrophomina phaseolina. Furthermore, the insight of such a ligninolytic enzyme will contribute to the assessment of its potentiality as a bioremediation tool.

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“…science, pharmaceutical science, and biological science [10][11][12][13][14][15][16][17]. In recent years, literatures have reported that hesperetin possesses the potential to behave as an effective inhibitor of thrombin-like serine proteases isolated from the venom of Crotalus simus snakes [18].…”

Section: Panda and Ehsanmentioning

confidence: 99%

Molecular Docking Studies of Snake Venom Serine Protease of Sharp-Nosed Pit Viper With Hesperetin

Panda¹,

Ehsan

2018

Asian J Pharm Clin Res

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Objective: The management of snake bite envenomation is a global challenge affecting millions of people. Immunotherapy is still regarded as the treatment of choice; however, their subsequent adverse effects restrict their potential use for therapy against snake venom poisoning. In recent years, more attention has been given to the exploration of indigenous medicinal plants for their outstanding benefits for the treatment of several diseases and disorders, including snake venom poisoning. Hesperetin is a naturally occurring compound derived from a flavanone glycoside, hesperidin and is obtained from various citrus fruits. It is known to possess significant inhibitory activity against snake venom serine proteases. The aim of our present study was to investigate the significant inhibitory action of hesperetin on thrombin-like serine protease from sharp-nosed pit viper (Deinagkistrodon acutus) snake venom. Methods:We have employed molecular docking analysis by implementing the state-of-the-art docking program to validate the hypothesis of the prospective inhibitory properties of hesperetin on thrombin-like serine proteases of snake venom. AutoDock 4.2, InterProSurf, MGLTools, and MTiAutoDock were utilized for the molecular docking analysis of thrombin-like serine protease obtained from the snake venom of sharp-nosed pit viper with the natural compound hesperetin. Results:The results generated from in silico based approach reveals the significant inhibitory role of hesperetin against thrombin-like snake venom proteases, which might lead to the drug designing of the inhibitors of snake venom serine proteases. Conclusion:The implementation of molecular docking analysis by the employment of state-of-the-art docking program supports the potential of inhibitory activity of naturally obtained hesperetin compound on thrombin-like serine proteases of snake venom. The generated in silico results suggests that the novel structure hesperetin -flavanone might act as a potent inhibitor of thrombin-like snake venom proteases, and unlocks the possibilities for designing drugs of the inhibitors of snake venom serine proteases. Moreover, the investigation of the novel compound obtained from natural sources for their inhibitory activity against snake venom serine proteases would lead to the discovery of newer inhibitory compound from a highly uninvestigated research arena.

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Physicochemical characterization and functional analysis of some snake venom toxin proteins and related non-toxin proteins of other chordates

Cited by 66 publications

References 17 publications

The Biophysical Characteristics and Structural Exploration of Programmed Cell Death Regulator B-Cell Lymphoma 2-Associated X Protein of Chinese Liver Fluke (Clonorchis Sinensis)

The Biophysical Characteristics and Structural Exploration of Programmed Cell Death Regulator B-Cell Lymphoma 2-Associated X Protein of Chinese Liver Fluke (Clonorchis Sinensis)

An insight into the lignin peroxidase of Macrophomina phaseolina

Molecular Docking Studies of Snake Venom Serine Protease of Sharp-Nosed Pit Viper With Hesperetin

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