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Designing of disruptor molecules to restrain the protein–protein interaction network of VANG1/SCRIB/NOS1AP using fragment-based drug discovery techniques

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Abstract

Governing protein–protein interaction networks are the cynosure of cell signaling and oncogenic networks. Multifarious processes when aligned with one another can result in a dysregulated output which can result in cancer progression. In the current research, one such network of proteins comprising VANG1/SCRIB/NOS1AP, which is responsible for cell migration, is targeted. The proteins are modeled using in-silico approaches, and the interaction is visualized utilizing protein–protein docking. Designing drugs for the convoluted protein network can serve as a challenging task that can be overcome by fragment-based drug designing, a recent game-changer in the computational drug discovery strategy for protein interaction networks. The model is exposed to the extraction of hotspots, also known as the restrained regions for small molecular hits. The hotspot regions are subjected to a library of generated fragments, which are then recombined and rejoined to develop small molecular disruptors of the macromolecular assemblage. Rapid screening methods using pharmacokinetic tools and 2D interaction studies resulted in four molecules that could serve the purpose of a disruptor. The final validation is executed by long-range simulations of 100 ns and exploring the stability of the complex using several parameters leading to the emergence of two novel molecules VNS003 and VNS005 that could be used as the disruptors of the protein assembly VANG1/SCRIB/NOS1AP. Also, the molecules were explored as single protein targets approbated via molecular docking and 100 ns molecular dynamics simulation. This concluded VNS003 as the most suitable inhibitor module capable of acting as a disruptor of a macromolecular assembly as well as acting on individual protein chains, thus leading to the primary hindrance in the formation of the protein interaction complex.

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Acknowledgements

We would like to dedicate our acknowledgment to the Department of Biosciences and Bioengineering, along with the Centre for Nanotechnology at IIT Guwahati. We would like to thank the School of Health Science and Technology, Param-Ishan, and BSL facilities of IIT Guwahati. Also, a sincere acknowledgment is directed toward Schrodinger and Senior Scientist Dr. Prajwal Nandekar, for licensing the use of the software.

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  1. Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 39, India

    Suchandra Roy Acharyya, Plaboni Sen, Thirukumaran Kandasamy & Siddhartha Sankar Ghosh

  2. Centre for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, 39, India

    Siddhartha Sankar Ghosh

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Acharyya, S.R., Sen, P., Kandasamy, T. et al. Designing of disruptor molecules to restrain the protein–protein interaction network of VANG1/SCRIB/NOS1AP using fragment-based drug discovery techniques. Mol Divers 27, 989–1010 (2023). https://doi.org/10.1007/s11030-022-10462-0

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