Docking Complexes of Active Phytochemicals with VK-deficient Genes

Title:Docking Complexes of Active Phytochemicals with VK-deficient Genes

Volume: 12 Issue: 3

Author(s): Shalini Rajagopal, Archa Nair, Rutuja Digraskar, Alekya Allu, Jalaja Naravula, Saji Menon, Sivaramaiah Nallapeta, Anil Kumar S, Sugunakar Vuree, G. Bhanuprakash Reddy, P.B. Kavi Kishor, Bipin G. Nair, Girinath G. Pillai, Prashanth Suravajhala*Renuka Suravajhala

Affiliation:

• Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana PO 690525, Kerala, India
• Bioclues.org, Hyderabad 500072, India

Abstract:

Background: Vitamin K (VK) deficiency occurs when the body does not have enough vitamin K to produce proteins that are essential for blood clotting and bone health. Vitamin K is a cofactor that plays a major role in various comorbidities. Over the years, efforts have been made to identify the interaction between natural compounds, such as K vitamers, that could play a significant role in regulation of the blood coagulation. We intended to obtain insights into the potential therapeutic implications of phytochemicals for treating VK deficiency-related diseases by investigating the interactions between phytochemicals and VK-deficient genes.s.

Methods: On active phytochemical docking complexes with VK-deficient genes, there is no specific information available as of yet. In this computationally aided docking study, we were interested in finding the pathogenic blood coagulation-related genes that are linked to VK deficiency. Based on literature reviews and databases, bioactive phytochemicals and other ligands were considered. To provide precise predictions of ligand-protein interactions, docking parameters and scoring algorithms were thoroughly optimized. We have performed molecular docking studies and observed the way the complexes interact.

Results: Specific binding interactions between active phytochemicals and VK pathogenic mutations have been identified by the docking study. Hydrogen bonds, van der Waals interactions, and hydrophobic contacts, which are indications of high binding affinities, have been observed in the ligand-protein complexes. Few phytochemicals have demonstrated the ability to interact with the targets of VK-deficient genes, indicating their capacity to modify pathways relevant to VK deficiency. The results of the docking study have explained the three pathogenic genes, viz. VWF, F8, and CFTR, wherein VWF and F8 play important roles in blood coagulation and people with cystic fibrosis, to have a deficiency in vitamin K. Thirty-five compounds from different plant and natural sources were screened through molecular docking, out of which two compounds have been considered as controls, including curcumin and warfarin (R-warfarin and S-warfarin), which are the most common anticoagulants readily available in the market. They act by inhibiting vitamin K epoxide reductase (VKOR), which is needed for the gamma-carboxylation of vitamin K-dependent factors.

Conclusion: A focus on other compounds, like theaflavin, ellagic acid, myricetin, and catechin was also made in this study as they show more binding affinity with the three pathogenic proteins. Based on the results, the complexes have been found to possess great potential and thus may be considered for further interaction studies. The potential for active phytochemicals to generate docking complexes with VK-deficient genes is highlighted in this computational analysis. Health disorders related to VK insufficiency may be significantly impacted by these interactions. To validate the expected interactions and determine the therapeutic potential of the identified phytochemicals, more experimental research, including in vitro and in vivo experiments, is needed.

Cite this article as:

Rajagopal Shalini, Nair Archa, Digraskar Rutuja, Allu Alekya, Naravula Jalaja, Menon Saji, Nallapeta Sivaramaiah, Kumar S Anil, Vuree Sugunakar, Reddy G. Bhanuprakash, Kishor Kavi P.B., Nair G. Bipin, Pillai G. Girinath, Suravajhala Prashanth*, Suravajhala Renuka, Docking Complexes of Active Phytochemicals with VK-deficient Genes, Current Biotechnology 2023; 12 (3) . https://dx.doi.org/10.2174/0122115501250686231017061958