Project title

CpHMDL simulations of pHLIP peptides: design of new tumor targeted drug delivery systems

Scientific Coordinator's name:

Miguel Ângelo Dos Santos Machuqueiro

Scientific Coordinator's e-mail:

mamachuqueiro@ciencias.ulisboa.pt

Principal R&D Unit:

Centro de Química e Bioquímica (CQB)

Other R&D Units involved in the project:

Instituto de Tecnologia Química e Biológica António Xavier (ITQB Nova)

Project keyword(s)

pH, protonation, molecular dynamics, lipid bilayer

Short abstract and comments

The long term goal for this project is to design pHLIP variants that retain full functionality but are selective to a specific pH range. Not all tumors exhibit the same pH profile and some of our human organs are inherently acidic (ex: kidneys). To be able to distinguish between different tumors and to separate them from our organs, we need a low pH switch in the peptide sequence that is able to prevent peptide insertion when the pH is too low. Therefore, we propose specific modifications in the peptide sequence to accommodate, for instance, a His residue which can work as a (too) low pH switch off. The technology based on this new family of peptides will be developed in collaboration with Prof. Engelman, Prof. Reshetnyak and Prof. Andreev (who is a consultant to this project) from Yale and Rhode Island Universities, USA. In the project short term, we will understand the molecular details of pH dependent peptide/membrane interaction and insertion, using our CpHMDL methodology. These processes are usually only followed indirectly in typical biophysical experiments and cannot be modeled using conventional methodologies, like molecular dynamics or continuum electrostatics due to the inherent complexity associated with pH. Using the CpHMDL method to study the interaction between a lipid bilayer and simple pentapeptides (usually used in pKa calibrations [Grimsley2009]) will provide valuable information on how pHsensitive amino acid side chains behave at the interface. For larger peptides like pHLIP, we will also develop a simpler approach based on the linear response approximation (LRA) for fast pKa calculations of the key Asp residues in pHLIP. We will also propose a steered MD protocol to circumvent sampling problems that might arise in the CpHMDL simulations of the pHLIP membrane insertion step. This will help us to bypass the kinetic barriers and traps, typical of processes happening at slower timescales. In biological membranes, the complexity of the membrane/water interface is much higher than in “in vitro” experiments. The presence of a myriad of different lipid molecules in their composition, including a significant amount of anionic head groups, will change drastically the electrostatic environment around pHLIP. In this proposal we will also evaluate how the lipid composition and characteristics influence the protonation profile of the peptide, taking in consideration that, under certain conditions, even lipids in the bilayer will be able to exchange protons.

Potential uses/indications

Design of new tumor targeted drug delivery systems