Emerging Tools and Next Generation Biophysics in Drug Discovery

Biophysical techniques like nuclear magnetic resonance are becoming increasingly prevalent in drug discovery, supporting the hit-to-lead process. However, it is only one of many methods being utilised within medicinal chemistry, with more and more novel techniques demonstrating advantages over the conventional methods of identifying drug candidates.  

Acoustic Ejection Mass Spectrometry

Mass spectrometry (MS) is not a new technique within medicinal chemistry and continues to play a significant part in drug discovery. MS enables researchers to explore biological specimens at a deeper level, “generating quantitative insight about their molecular contents”. 

In a typical MS experiment, molecules within a sample are fragmented and specified based on their mass and electrical charge, giving a m/z value. Unfortunately, conventional MS methods demonstrate a number of limitations – liquid chromatography (LC) is often used to support MS in the case of aqueous samples, however, it has been noted that for targeted analysis, use of LC greatly limits MS throughput and performance. 

Acoustic ejection mass spectrometry (AEMS) is a novel sample delivery approach to characterising molecules. AEMS comprises two critical components which facilitate molecular analysis. The first part is the acoustic droplet ejection module, which uses focused acoustic energy to eject sample droplets out of the standard microplates in which the samples are placed upon.

The second part of AEMS is the open-port interface (OPI), which is positioned above the microplate. According to an article, the “continuous liquid flow in OPI captures the acoustically dispensed sample droplets and delivers it to the standard ESI-MS for the high-throughput readout”. ESI-MS (electrospray ionisation mass spectrometry) is simply another type of mass spectrometry. 

One of the main advantages for AEMS in drug discovery is speed – in comparison with the conventional LC-MS technology, which is considered the gold-standard, AEMS has been suggested to process molecules much faster. The sample readout has been described as “an order of magnitude faster” than LC-MS which is beneficial for researchers, as it allows them to process a larger number of samples in a smaller period of time, so less time-intensive. 

Another important benefit of AEMS is that the sample preparation and method development is greatly simplified. This again contributes to an accelerated process which enables the assay-turnaround time to be significantly reduced, saving time and money for pharma companies. 

The high-speed, high-throughput analysis has seen AEMS become a focus for attention in the drug discovery arena. The robust technique and ability to analyse unprocessed samples with minimal methods, while facilitating preservation of the original samples are desirable characteristics in mass spectrometry, especially when dealing with complex biological samples which are often unprocessed.  

AEMS is a relatively new method in terms of implementation in drug discovery, hence, there is a limited amount of literature with regards to disadvantages. However, as an increasing number of researchers investigate the pros vs cons in drug discovery, it will soon become evident the success of this analytic technique.  

Surface Plasmon Resonance

Surface plasmon resonance (SPR) has been described as a “biophysical approach used to investigate biomolecular interactions between two or more molecules”. This technique is extremely diverse, and can be used to characterise a wide range of biological molecules, from ions to proteins to microorganisms like viruses. 

SPR systems commercially available comprised a microfluidic setup, an optical system, and an electronic system. The optical system in particular is used to analyse surface biochemical activity. Standard SPR assays work by “measuring the target-induced change in reflectivity of a planar gold surface as a function of refractive index change”. 

One of the major benefits of SPR is the fact it is not a label-free technique and does not require additional reagents, assays, or labour-intensive sample preparation. While SPR is emerging in drug discovery, it has been implemented in other biological investigations. An SPR immunosensor was developed to detect the salmonella pathogen in contaminated water: in this case, the orientation of antibody immobilised on the sensor surface is crucial to increase the activity of the antibody interacting with the analyte of interest. 

This was suggested to improve the sensitivity and detection of very low concentrations of antigens. In immunological drug discovery, this could be a very useful tool due to identifying potential drug targets with a higher resolution than perhaps other techniques. 

Orbitrap mass spectrometry

Orbitrap mass spectrometry is considered one of the newest mass analysers based on the separation of ions in an oscillating electric field. It consists of an outer and central electrode to which electrostatic fields are applied. The m/z value is said to be derived from the frequency of the harmonic ion oscillations along the axis of the electric field. 

Fourier-transform of the signals induced in the outer electrode provides the mass spectrum of the trapped ions, which provides more information about the molecules. The potential advantages of this technique include (1) a high mass resolving power, (2) increased space-charge capacity at higher masses, (3) high mass accuracy, (4) high dynamic range.

It has been suggested that the impressive reliability and low maintenance cost of OMS instruments have become an attractive platform for proteomic experiments. In addition, the high resolution and accurate mass detection would be especially beneficial for proteomics in the case of qualitative and quantitative analyses. 

Currently, proteomics relies mainly on a bottom-up approach to mass spectrometry (BU-MS) for protein-level analysis. Unfortunately, there are a number of challenges to this approach. According to a recent review, BU-MS relies upon the breakdown of proteins into peptides 5 to 20 amino acids long before identification. As a result, the database searches match only fragments to entire proteins – a process that is frustrated by the sequence homology or similarity shared by the proteins.

Accelerating the drug discovery process is key to addressing the increasing demand for medicines as the global population (and chronic diseases) continues to grow. Emerging biophysics techniques demonstrate a number of advantages which could support this, and introduce methods of characterising molecules with greater resolution on a shorter time-scale and at a lower cost.  

Charlotte Di Salvo, Editor & Lead Medical Writer
PharmaFeatures