Periodic Reporting for period 1 - Lipopeutics (Functional Lipid−Protein Interactions in Integral Membrane Proteins)
Período documentado: 2020-11-01 hasta 2022-10-31
The MSCA fellowship ‘Lipopeutics’ focusses on membrane proteins – a class of proteins that make up a third of the human proteome and perform a significant role in a plethora of cellular functions including signalling, molecular transport, cellular adhesion and even cell death. This importance of membrane proteins to physiological function is exemplified by recent genomic studies identifying nearly 200,000 disease associated mutations within them. Considering this significance, enormous academic and industrial efforts have been focussed on these proteins over the past decades. However, membrane proteins still makeup nearly 60% of all current drug targets and limited novel drugs for them have been developed.
Despite the pharmaceutical impasse, significant experimental headway has been made in deciphering the underlying functional basis of these proteins. The phospholipids within the cellular membrane were long thought to ‘merely’ anchor the protein. However, advances in electron microscopy and mass-spectrometry methods have identified the lipids to be active modulators of protein function. The scientific objective of the Lipopeutics project is to rationalize this endogenous lipid modulation of protein function to design novel hydrophobic drugs.
To achieve the overarching scientific objective, the project was divided into four specific subobjectives each ascribed to its own Work Package. (1) Firstly, interaction sites of specific lipids within the protein structure needed to be identified. (2) Subsequently, the role of this lipid/binding-site in the modulation of protein function needed to be validated. (3) Then, hydrophobic lipid-like drug molecules capable of binding at the sites need to be identified. (4) Finally, the chemical structures of the identified drug molecules need to be optimized.
Despite the pharmaceutical impasse, significant experimental headway has been made in deciphering the underlying functional basis of these proteins. The phospholipids within the cellular membrane were long thought to ‘merely’ anchor the protein. However, advances in electron microscopy and mass-spectrometry methods have identified the lipids to be active modulators of protein function. The scientific objective of the Lipopeutics project is to rationalize this endogenous lipid modulation of protein function to design novel hydrophobic drugs.
To achieve the overarching scientific objective, the project was divided into four specific subobjectives each ascribed to its own Work Package. (1) Firstly, interaction sites of specific lipids within the protein structure needed to be identified. (2) Subsequently, the role of this lipid/binding-site in the modulation of protein function needed to be validated. (3) Then, hydrophobic lipid-like drug molecules capable of binding at the sites need to be identified. (4) Finally, the chemical structures of the identified drug molecules need to be optimized.
Research over the course of the MSCA fellowship was carried out through four different Work Packages (WP) designed to achieve the scientific objectives in a phase-wise manner. In WP1, to identify specific lipid molecules bound within the transmembrane domains of the proteins, coarse-grain molecular dynamics simulations were utilized. This led to the identification of unique lipid sites within the Erwinia chrysanthemi ligand-gated ion channel and Kv3.1 voltage-gated potassium channel. In WP2, a Markov-state-Model capable of distinguishing drug binding poses and their impacts on protein conformations was developed. In WP3, ligand-based and structure-based virtual screening was used to identify the possible modulators of the Kv7 voltage-gated Potassium channel. Finally, in WP4, non-equilibrium molecular dynamics simulations were used to identify the accessibility of the designed drug molecules to the Kv7 Potassium channel and the GABAA pentameric ligand-gated ion channel.
The systematic computational approach led to significant research outcomes that were disseminated to both scientific and general audiences. The work yielded four publications in open-access peer-reviewed journals with three more underway. Additionally, the work was presented at five scientific conferences across Europe and America. The pharmaceutical results of the projects identifying the binding sites and interaction mechanisms are currently being taken forward in ongoing drug design projects.
The systematic computational approach led to significant research outcomes that were disseminated to both scientific and general audiences. The work yielded four publications in open-access peer-reviewed journals with three more underway. Additionally, the work was presented at five scientific conferences across Europe and America. The pharmaceutical results of the projects identifying the binding sites and interaction mechanisms are currently being taken forward in ongoing drug design projects.
The piecewise distribution of the project in four scientific subobjectives allowed progress beyond the state of the art along scientific, technical, and pharmaceutical aspects. Firstly, the identification of lipid/drug binding sites and their effects on protein structure/function enhanced scientific understanding of the functioning of ion channels. With the predominance of ion channels in a range of cellular functions, the results can translate into better understanding of a host of physiological processes.
Secondly, the project made significant technical progress advancing the field of multiple computational modelling techniques. Markov state modelling techniques have thus far been primarily found use in understanding protein folding and conformational mechanisms. However, in WP2 the project devised a methodology for its use to study drug binding. Additionally, in WP4, the project demonstrated a novel use of the state-of-the-art Martini 3 coarse grain force field to identify drug binding pockets in an automated unbiased manner. These methodologies will find considerable use for computational biophysicists in upcoming years.
Finally, the project identified the mechanistic and pharmacophoric basis of drug action within two important ion channels – the GABAA pentameric ligand-gated and Kv7 tetrameric voltage-gated channels. Pharmaceutically, the channels are implicated in a host of diseases including epilepsy, depression and anxiety and these results open avenues for the development of novel drugs targeting them.
Secondly, the project made significant technical progress advancing the field of multiple computational modelling techniques. Markov state modelling techniques have thus far been primarily found use in understanding protein folding and conformational mechanisms. However, in WP2 the project devised a methodology for its use to study drug binding. Additionally, in WP4, the project demonstrated a novel use of the state-of-the-art Martini 3 coarse grain force field to identify drug binding pockets in an automated unbiased manner. These methodologies will find considerable use for computational biophysicists in upcoming years.
Finally, the project identified the mechanistic and pharmacophoric basis of drug action within two important ion channels – the GABAA pentameric ligand-gated and Kv7 tetrameric voltage-gated channels. Pharmaceutically, the channels are implicated in a host of diseases including epilepsy, depression and anxiety and these results open avenues for the development of novel drugs targeting them.