Sade Lamidi's Research Blog

The aim of this research is to develop theoreticl knowledge on photosensitizer binding to amyloids and to apply the outcome in prospective experimental analysis. 

The overarching goal is to develop a hybrid drug delivery system containing photosensitizer binding to amyloids inside liquid condensates. The photosensitizer to be used has Aggregation induced emission (AIE) characteristics such that it becomes a photoactive sensitizer or triplet oxygen on binding to amyloid domain. 

The theoretical analysis centers around, looking at conformational changes in the pi-conjugated photosensitizers upon binding to amyloidal domains. The idea is to look for pi-ring planarization that would increase aromatization in the molecule and hence make it photoactive (Fig. 1). This change can be experimentally observed in emission spectroscopy. During the study various photosensitizers and amyloid combinations will be studied for optimized results. 

Detailing further, we will synthesize dyes and mix them into condensates containing fibers. We will observe binding properties of the dyes and correlate those properties with the strength of interactions with the amyloid fibers. Fluorescent light emission will be the guiding parameter along with the production of reactive oxygen species. Computationally, structural modifications will be made to the dye based on binding efficiency and conformation of the dyes when interacting with the fibers. The new dye candidates will be tested. The targeted fibers are hydrophobic, so we will be increasing the conjugation of the dye which in return will increase the hydrophobicity allowing for better interaction between the dye and fibers. This experimental analysis and computational results will be interchangeable, allowing for the application of computational lessons to experiments. Our end goal will be to produce reactive oxygen species by generating novel high efficiency photosensitizers, which will be killing cancer cells and activating the prodrug.

Fig 2. Variation of torsional angle 1 in PS1 as observed in simulation frames. Inset shows the molecular structure with relevant benzene planes marked.

Fig 3. Variation of torsional angle 2 in PS1 as observed in simulation frames. Inset shows the molecular structure with relevant benzene planes marked.

Fig 4. Variation of torsional angle 1 vs angle 2 in PS1 as observed in simulation frames. Inset shows the molecular structure with relevant benzene planes marked.

Computational Methods

Appropriate tutorials were completed through Maestro Schrödinger to gain familiarity with computation modeling.

Molecular dynamics, Conformational dynamics to prepare three- dimensional dye and amyloid

Amyloid structure obtained from the Protein Data Bank was utilized until a more comprehensive understanding of dye binding is achieved

Desmond system builder used to simulate PS1 in water, using SPC water model containing fixed partial charges, bond lengths, and three interaction sites. High aggregation, linked to higher emission intensity and efficient binding is observed when dye interacts with water versus when bound to previously tested solvent THF 1. It is predicted that dye will better bind to the LVFFAR9 beta sheet than it does water.

Using the SPC simulation, we then observed and calculated the geometric parameters of the two aromatic moieties on PS1 by measuring the dihedral angles upon aggregation. One dimensional histogram was created for each given angle (l and r) on PS1.

To calculate probability of planarity of molecules, a dimensional statistical analysis was done (Fig. 2-4).

5/30/2024

• After evaluation of angles 1 and 2, it is important to include angle three binding the two

• phenyl rings, out of plane with the remainder of the molecule. Because this portion of the

• molecule is out of plane it requires a relaxed torsional scan.

• To do so a third histogram is to be calculated. Because angle three does not have as significant of a correlation with the remainder of the molecule

• Due to symmetry, there is low correlation between angles 1 and 2, and

• changing them doesn't require the neighboring hydrogen atoms to move so rigid

• scans will be performed, first.

• On angle 3 a relaxed scan will be performed.

Questions:
1. When considering the third angle, what is the energy of each trajectory possible?

Summer 2024

• start of TTPM syntehsis 

• we started by synthesizing 4-pyradilne-iodo-benzene. To do so a suzuki recation is done under heated conditions of 72 degrees celcius. 

• 7/15- Suzuki reaction/sample TLC 

Appropriate glassware was warmed in the RV for 5 days, to avoid water disturbing the reaction. 1-bromo-iodo-benzene (0.552 g), pyridine baronic acid (0.200g), and Pottasium phosphate (1.04g) was added into a double neck round bottom flask, one end sealed and one end containing a gas adapter. 16mL of DMF, sealed and dried by molecular seeds was nirtogentaed and added to A, B, and C inside of the double headed round bottom flask. Distilation glassware, warmed for 5 days in RV was set up. To assebmle, tale and a heck clamp was attatched and a heat sensor sat in the bowl containig the round bottom flask. The solution was degassed for thirty minutes. The method of nitrogenation we chose for the DMF solution was piercing a needle attatche to  a nitrogen filled ballon throuygh the sealed piercable  bottle lid. To degas the reaction, a needle connected to a syringe and tube was pierced into the sealed end of the flask. Nitrogen flowed through the tube at a pressure of 10 psi.  On the other head of the round bottom, a  gas adapter was switched on allowing for Oxygen to exit the recation as Nitrogen flowed in.  Bubbling of the solution signified successful degassing.  After degassing the catalyst was added 

References:

1. Zhuang, W., Yang, L., Ma, B., Kong, Q., Li, G., Wang, Y., & Ben Zhong Tang. (2019). Multifunctional Two-Photon AIE Luminogens for Highly Mitochondria-Specific Bioimaging and Efficient Photodynamic Therapy. ACS Applied Materials & Interfaces, 11(23), 20715–20724. https://doi.org/10.1021/acsami.9b04813

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