An immersive journey to the molecular structure of SARS-CoV-2: Virtual reality in COVID-19

Molecular Docking Improved with Human Spatial Perception Using Virtual Reality

Adaptive steered molecular dynamics (ASMD) is a computational biophysics method in which an external force is applied to a selected set of atoms or a specific reaction coordinate to induce a particular molecular motion. Virtual reality (VR) based methods for protein-ligand docking are beneficial for visualizing on-the-fly interactive molecular dynamics and performing promising docking trajectories. In this paper, we propose a novel method to guide ASMD with optimal trajectories collected from human experiences using interactive molecular dynamics in virtual reality (iMD-VR). We also explain the benefits of using VR as a tool for expediting the process of ligand binding, outlining an experimental protocol that enables iMD-VR users to guide Amprenavir into and out of the binding pockets of HIV-1 protease and recreate their respective crystallographic binding poses within 5 minutes. Later, we discuss our analysis of the results from iMD-VR-assisted ASMD simulation and assess its performance compared to a standard ASMD simulation. From the accuracy point of view, our proposed method calculates higher Potential Mean Force (PMF) values consistently relative to a standard ASMD simulation with an almost twofold increase in all the experiments. Finally, we describe the novelty of the research and discuss results showcasing a faster and more effective convergence of the ligand to the protein's binding site as compared to a standard molecular dynamics simulation, proving the effectiveness of VR in the field of drug discovery. Future work includes the development of an artificial intelligence algorithm capable of predicting optimal binding trajectories for many protein-ligand pairs, as well as the required force needed to steer the ligand to follow the said trajectory.

The emerging potential of interactive virtual reality in drug discovery

INTRODUCTION

The potential of virtual reality (VR) to contribute to drug design and development has been recognized for many years. A recent advance is to use VR not only to visualize and interact with molecules, but also to interact with molecular dynamics simulations 'on the fly' (interactive molecular dynamics in VR, IMD-VR), which is useful for flexible docking and examining binding processes and conformational changes.

AREAS COVERED

The authors use the term 'interactive VR' to refer to software where interactivity is an inherent part of the user VR experience e.g. in making structural modifications or interacting with a physically rigorous molecular dynamics (MD) simulation, as opposed to using VR controllers to rotate and translate the molecule for enhanced visualization. Here, they describe these methods and their application to problems relevant to drug discovery, highlighting the possibilities that they offer in this arena.

EXPERT OPINION

The ease of viewing and manipulating molecular structures and dynamics, using accessible VR hardware, and the ability to modify structures on the fly (e.g. adding or deleting atoms) - and for groups of researchers to work together in the same virtual environment - makes modern interactive VR a valuable tool to add to the armory of drug design and development methods.

Bioinformatics and the Metaverse: Are We Ready?

COVID-19 forced humanity to think about new ways of working globally without physically being present with other people, and eXtended Reality (XR) systems (defined as Virtual Reality, Augmented Reality and Mixed Reality) offer a potentially elegant solution. Previously seen as mainly for gaming, commercial and research institutions are investigating XR solutions to solve real world problems from training, simulation, mental health, data analysis, and studying disease progression. More recently large corporations such as Microsoft and Meta have announced they are developing the Metaverse as a new paradigm to interact with the digital world. This article will look at how visualization can leverage the Metaverse in bioinformatics research, the pros and cons of this technology, and what the future may hold.

Virtual reality adoption during the COVID-19 pandemic: A uses and gratifications perspective

The coronavirus disease 2019 (COVID-19) pandemic has impacted all aspects of people's lives, including how we work, play, learn, exercise, and socialize. Virtual reality (VR) technology has the potential to mitigate many of the challenges brought about by the pandemic, which has spurred increased adoption. However, relatively low adoption overall and limited software still restrict the power of VR to address COVID-19 difficulties effectively. This study examines how the perceived impacts of COVID-19 might lead to different VR uses and gratifications and device ownership / variability. Furthermore, we investigate the importance of social interactivity within VR for increasing adoption intentions.

We surveyed 298 Amazon Mechanical Turk users during the Fall of 2020. Results indicate that the pandemic's perceived impacts influenced the likelihood of acquiring VR for education, tourism, and work. For VR ownership and variability, those who purchased VR during the pandemic were more likely to report buying it for work. Those with access to high-end VR hardware were more likely to report a broader range of uses, including socializing, health, and telemedicine. Validating the importance of various applications during the pandemic, we found that the desire for social interactivity mediates the impacts of COVID-19 on future adoption intentions. Theoretically, we propose several gratifications sought via the use of VR during the pandemic. Practically, we discuss recommendations for future VR research, marketing, and software design.

Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease

The main protease (Mpro) of the SARS-CoV-2 virus is one focus of drug development efforts for COVID-19. Here, we show that interactive molecular dynamics in virtual reality (iMD-VR) is a useful and effective tool for creating Mpro complexes. We make these tools and models freely available. iMD-VR provides an immersive environment in which users can interact with MD simulations and so build protein complexes in a physically rigorous and flexible way. Recently, we have demonstrated that iMD-VR is an effective method for interactive, flexible docking of small molecule drugs into their protein targets (Deeks et al. PLoS One 2020, 15, e0228461). Here, we apply this approach to both an Mpro inhibitor and an oligopeptide substrate, using experimentally determined crystal structures. For the oligopeptide, we test against a crystallographic structure of the original SARS Mpro. Docking with iMD-VR gives models in agreement with experimentally observed (crystal) structures. The docked structures are also tested in MD simulations and found to be stable. Different protocols for iMD-VR docking are explored, e.g., with and without restraints on protein backbone, and we provide recommendations for its use. We find that it is important for the user to focus on forming binding interactions, such as hydrogen bonds, and not to rely on using simple metrics (such as RMSD), in order to create realistic, stable complexes. We also test the use of apo (uncomplexed) crystal structures for docking and find that they can give good results. This is because of the flexibility and dynamic response allowed by the physically rigorous, atomically detailed simulation approach of iMD-VR. We make our models (and interactive simulations) freely available. The software framework that we use, Narupa, is open source, and uses commodity VR hardware, so these tools are readily accessible to the wider research community working on Mpro (and other COVID-19 targets). These should be widely useful in drug development, in education applications, e.g., on viral enzyme structure and function, and in scientific communication more generally.