Neurodegenerative diseases (NDDs), such as Parkinson's disease and Alzheimer's disease present a significant global health concern. The misfolding of proteins from native disordered monomeric forms into beta-sheet enriched aggregates of oligomers and fibrils is a core hallmark of NDDs. Novel methods that detect such preclinical structural protein biomarkers are vital for early diagnosis, disease progression monitoring and drug screening. Mid-infrared spectroscopy can provide structural-sensitive detection of proteins by accessing their unique absorption signatures. Plasmonic surface-enhanced infrared absorption (SEIRA) spectroscopy employs nanoplasmonics to advance biosensing capabilities and develop an infrared structural protein biomarker-based biosensor for NDDs.

In the first original contribution of the thesis, the capabilities of plasmonic SEIRA as a diagnostic tool for NDDs are explored. The study introduces a novel sensor - ImmunoSEIRA, an optofluidic nanoplasmonic infrared metasurface sensor that detects alpha-synuclein (aSyn), a structural protein biomarker for NDDs. The sensor performs structural profiling of different aSyn species - monomers, oligomers and fibrils using their unique absorption signatures from minute sample volumes with specificity. The sensor is coupled with artificial intelligence to enable unprecedented quantitative prediction of oligomers and fibrils in their mixture. The sensor also performs multiplexed detection of different NDDs biomarkers simultaneously from the same sample and can retrieve pathological biomarker fingerprints in the presence of complex biomatrix.

The second contribution is developing a novel nanoplasmonic infrared microarray sensor for label-free, high-throughput drug screening based on structural protein biomarkers in NDDs. The sensor features 2D plasmonic metasurface arrays as sensing units for enhanced sensing of secondary structure of proteins and high-throughput detection is enabled by precise micropatterning of polymeric honeycomb-shaped structures enclosing them to form microwells. Versatile sensor designs with 48, 96 and 384 microwells are realized and a detection sensitivity from minute protein samples of 7 nanograms is achieved. The sensor screened 11 drug compounds, evaluating their inhibiting effect on aSyn aggregation by quantitatively identifying different secondary structural forms in the mixture, even when it predominantly contained oligomers, where current assays fail.

Finally, a nanoplasmonic sensor for chemical imaging of ultra-thin tissues by optical photothermal infrared spectroscopy is presented for the diagnostic and mechanistic understanding of diseases like cancer and NDDs. The study designed a 2D plasmonic nanoslit platform to extract the amplified infrared absorption fingerprints from ultra-thin tissue samples by exploiting the near-field enhancement, visualized using O-PTIR tool. A working protocol is realized to prepare and transfer ultra-thin tissues (100 nm) to the sensor using resin embedding and ultramicrotome sectioning. Finally, proof-of-concept retrieval of protein absorption fingerprints from a 100 nm thin model tissue sample with sub-micron resolution using the O-PTIR tool is presented.

The sensors developed in this thesis are the outcomes of interdisciplinary research incorporating versatile technologies, offering promising advancements toward realizing novel methods for the mechanistic understanding, diagnosis and drug screening of NDDs.