Interactive Molecular Dynamics: Scaling up to Large Systems

Interactive molecular dynamics in virtual reality for modelling materials and catalysts

Interactive molecular dynamics simulation in virtual reality (iMD-VR) is emerging as a promising technique in molecular science. Here, we demonstrate its use in a range of fifteen applications in materials science and heterogeneous catalysis. In this work, the iMD-VR package Narupa is used with the MD package, DL_POLY [1]. We show how iMD-VR can be used to: (i) investigate the mechanism of lithium fast ion conduction by directing the formation of defects showing that vacancy transport is favoured over interstitialcy mechanisms, and (ii) guide a molecule through a zeolite pore to explore diffusion within zeolites, examining in detail the motion of methyl n-hexanoate in H-ZSM-5 zeolite and identifying bottlenecks restricting diffusion. iMD-VR allows users to manipulate these systems intuitively, to drive changes in them and observe the resulting changes in structure and dynamics. We make these simulations available, as a resource for both teaching and research. All simulation files, with videos, can be found online (https://doi.org/10.5281/zenodo.8252314) and are provided as open-source material.

W254 in furin functions as a molecular gate promoting anti-viral drug binding: Elucidation of putative drug tunneling and docking by non-equilibrium molecular dynamics

Furins are serine endoproteases that process precursor proteins into their biologically active forms, and they play essential roles in normal metabolism and disease presentation, including promoting expression of bacterial virulence factors and viral pathogenesis. Thus, furins represent vital targets for development of antimicrobial and antiviral therapeutics. Recent experimental evidence indicated that dichlorophenyl (DCP)-pyridine "BOS" drugs (e.g., BOS-318) competitively inhibit human furin by an induced-fit mechanism in which tryptophan W254 in the furin catalytic cleft (FCC) functions as a molecular gate, rotating nearly 180o through a steep energy barrier about its chi-1 dihedral to an "open" orientation, exposing a buried (i.e., cryptic) hydrophobic pocket 1. Once exposed, the non-polar DCP group of BOS-318, and similar halo-phenyl groups of analogs, enter the cryptic pocket, stabilizing drug binding. Here, we demonstrate flexible-receptor docking of BOS-318 (and various analogs) was unable to emulate the induced-fit motif, even when tryptophan was replaced with less bulky phenylalanine or glycine. While either substitution allowed access to the hydrophobic pocket for most ligands tested, optimal binding was observed only for W254, inferring a stabilizing effect of the indole sidechain. Furthermore, non-equilibrium steered molecular dynamics (sMD) in which the bound drugs (or their fragments) were extracted from the FCC did not cause closure of the open W254 gate, consistent with the thermodynamic stability of the open or closed W254 orientations. Finally, interactive molecular dynamics (iMD) revealed two putative conduits of drug entry and binding into the FCC, each coupled with W254 dihedral rotation and opening of the cryptic pocket. The iMD simulations further revealed ligand entry and binding in the FCC is likely driven in part by energy fluxes stemming from disruption and re-formation of ligand and protein solvation shells during drug migration from the solution phase into the FCC.

Co-creation environment with cloud virtual reality and real-time artificial intelligence toward the design of molecular robots

This paper describes the design philosophy for our cloud-based virtual reality (VR) co-creation environment (CCE) for molecular modeling. Using interactive VR simulation can provide enhanced perspectives in molecular modeling for intuitive live demonstration and experimentation in the CCE. Then the use of the CCE can enhance knowledge creation by bringing people together to share and create ideas or knowledge that may not emerge otherwise. Our prototype CCE discussed here, which was developed to demonstrate our design philosophy, has already enabled multiple members to log in and touch virtual molecules running on a cloud server with no noticeable network latency via real-time artificial intelligence techniques. The CCE plays an essential role in the rational design of molecular robot parts, which consist of bio-molecules such as DNA and protein molecules.

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.

MOF-VR: A Virtual Reality Program for Performing and Visualizing Immersive Molecular Dynamics Simulations of Guest Molecules in Metal-Organic Frameworks

Molecular dynamics simulations are useful to study diffusion of guest molecules in metal-organic frameworks. The interpretation of the generated three-dimensional trajectories is often difficult, because most visualization tools only allow two-dimensional projections. To facilitate interpretation, we present MOF-VR: a virtual reality program for performing interactive molecular dynamics simulations in metal-organic frameworks and visualizing atomic or molecular trajectories. MOF-VR consists of three subroutines: a construction routine to create hypothetical metal-organic frameworks by hand, a molecular dynamics suite, and a trajectory visualizer. To the best of our knowledge, MOF-VR is the first virtual reality program that allows hypothetical metal-organic frameworks to be constructed and tested in molecular dynamics simulations of guest molecules. We further show that MOF-VR is capable of performing state-of-the-art molecular dynamics simulations of guest molecules in rigid metal-organic frameworks in virtual reality and provides reliable simulation results.

Exploring human-guided strategies for reaction network exploration: Interactive molecular dynamics in virtual reality as a tool for citizen scientists

The emerging fields of citizen science and gamification reformulate scientific problems as games or puzzles to be solved. Through engaging the wider non-scientific community, significant breakthroughs may be made by analyzing citizen-gathered data. In parallel, recent advances in virtual reality (VR) technology are increasingly being used within a scientific context and the burgeoning field of interactive molecular dynamics in VR (iMD-VR) allows users to interact with dynamical chemistry simulations in real time. Here, we demonstrate the utility of iMD-VR as a medium for gamification of chemistry research tasks. An iMD-VR "game" was designed to encourage users to explore the reactivity of a particular chemical system, and a cohort of 18 participants was recruited to playtest this game as part of a user study. The reaction game encouraged users to experiment with making chemical reactions between a propyne molecule and an OH radical, and "molecular snapshots" from each game session were then compiled and used to map out reaction pathways. The reaction network generated by users was compared to existing literature networks demonstrating that users in VR capture almost all the important reaction pathways. Further comparisons between humans and an algorithmic method for guiding molecular dynamics show that through using citizen science to explore these kinds of chemical problems, new approaches and strategies start to emerge.

Computational methods for exploring protein conformations

Proteins are dynamic molecules that can transition between a potentially wide range of structures comprising their conformational ensemble. The nature of these conformations and their relative probabilities are described by a high-dimensional free energy landscape. While computer simulation techniques such as molecular dynamics simulations allow characterisation of the metastable conformational states and the transitions between them, and thus free energy landscapes, to be characterised, the barriers between states can be high, precluding efficient sampling without substantial computational resources. Over the past decades, a dizzying array of methods have emerged for enhancing conformational sampling, and for projecting the free energy landscape onto a reduced set of dimensions that allow conformational states to be distinguished, known as collective variables (CVs), along which sampling may be directed. Here, a brief description of what biomolecular simulation entails is followed by a more detailed exposition of the nature of CVs and methods for determining these, and, lastly, an overview of the myriad different approaches for enhancing conformational sampling, most of which rely upon CVs, including new advances in both CV determination and conformational sampling due to machine learning.

Novel Dihydropyrimidinone-Derived Selenoesters as Potential Cytotoxic Agents to Human Hepatocellular Carcinoma: Molecular Docking and DNA Fragmentation

BACKGROUND AND OBJECTIVE

Evidence point out promising anticancer activities of Dihydropyrimidinones (DHPM) and organoselenium compounds. This study aimed to evaluate the cytotoxic and antiproliferative potential of DHPM-derived selenoesters (Se-DHPM), as well as their molecular mechanisms of action.

METHODS

Se-DHPM cytotoxicity was evaluated against cancer lines (HeLa, HepG2, and MCF-7) and normal cells (McCoy). HepG2 clonogenic assay allowed verifying antiproliferative effects. The propidium iodide/ orange acridine fluorescence readings showed the type of cell death induced after treatments (72h). Molecular simulations with B-DNA and 49H showed docked positions (AutoDock Vina) and trajectories/energies (GROMACS). In vitro molecular interactions used CT-DNA and 49H applying UV-Vis absorbance and fluorescence. Comet assay evaluated DNA fragmentation of HepG2 cells. Flow cytometry analysis verified HepG2 cell cycle effects. Levels of proteins (β-actin, p53, BAX, HIF-1α, γH2AX, PARP-1, cyclin A, CDK-2, and pRB) were quantified by immunoblotting.

RESULTS

Among Se-DHPM, 49H was selectively cytotoxic to HepG2 cells, reduced cell proliferation, and increased BAX (80%), and p53 (66%) causing apoptosis. Molecular assays revealed 49H inserted in the CT-DNA molecule causing the hypochromic effect. Docking simulations showed H-bonds and hydrophobic interactions, which kept the ligand partially inserted into the DNA minor groove. 49H increased the DNA damage (1.5 fold) and γH2AX level (153%). Besides, treatments reduced PARP-1 (60%) and reduced pRB phosphorylation (21%) as well as decreased cyclin A (46%) arresting cell cycle at the G1 phase.

CONCLUSION

Together all data obtained confirmed the hypothesis of disruptive interactions between Se-DHPM and DNA, thereby highlighting its potential as a new anticancer drug.

A Web-Based Tool for Simulating Molecular Dynamics in Cloud Environments

Molecular dynamics simulations take advantage of supercomputing environments, e.g., to solve molecular systems composed of millions of atoms. Supercomputers are increasing their computing and memory power while they are becoming more complex with the introduction of Multi-GPU environments. Despite these capabilities, the molecular dynamics simulation is not an easy process. It requires properly preparing the simulation data and configuring the entire operation, e.g., installing and managing specific software packages to take advantage of the potential of Multi-GPU supercomputers. We propose a web-based tool that facilitates the management of molecular dynamics workflows to be used in combination with a multi-GPU cloud environment. The tool allows users to perform data pipeline and run the simulation in a cloud environment, even for those who are not specialized in the development of molecular dynamics simulators or cloud management.

Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes

Molecular dynamics (MD) simulations are increasingly used to elucidate relationships between protein structure, dynamics, and their biological function. Currently, it is extremely challenging to perform MD simulations of large-scale structural rearrangements in proteins that occur on millisecond timescales or beyond, as this requires very significant computational resources, or the use of cumbersome "collective variable" enhanced sampling protocols. Here, we describe a framework that combines ensemble MD simulations and virtual reality visualization (eMD-VR) to enable users to interactively generate realistic descriptions of large amplitude, millisecond timescale protein conformational changes in proteins. Detailed tests demonstrate that eMD-VR substantially decreases the computational cost of folding simulations of a WW domain, without the need to define collective variables a priori. We further show that eMD-VR generated pathways can be combined with Markov state models to describe the thermodynamics and kinetics of large-scale loop motions in the enzyme cyclophilin A. Our results suggest eMD-VR is a powerful tool for exploring protein energy landscapes in bioengineering efforts.

Molecular docking and molecular dynamics simulation studies on the adsorption/desorption behavior of bone morphogenetic protein-7 on the β-tricalcium phosphate surface

The adsorption/desorption behavior, and conformational and orientational changes of proteins on the surface of biomaterials are significant parameters for understanding how biomaterials perform their biological functions. In this study, for the first time, the interactions between BMP-7 and β-TCP (001) surface models with different ion-rich terminations (Ca-rich and P-rich) were investigated by molecular dynamics simulation (MD) and steered molecular dynamics simulation (SMD). The results indicated that BMP-7 preferentially interacts with both Ca-rich and P-rich β-TCP (001) surfaces at its wrist epitope residues with certain conformational changes, which led to more exposure of BMP-7 knuckle epitope residues to the environment and facilitation for binding to the type II receptor. Compared to the P-rich surface, it is speculated that the Ca-rich surface was more conducive to BMP-7 signal transduction since the upright orientation of the protein adsorption would lead to smaller hindrance for receptor binding. This study provided more atomistic and molecular information for better understanding the process of Ca-P surfaces affecting BMP-7 biological properties and further interpreted the osteoinductive mechanism from the perspective of growth factor adsorption. Moreover, the docking screening method adopted in this study is of guiding significance to the design and development of bioactive materials.

Nano for the Public: An Exploranation Perspective

Public understanding of contemporary scientific issues is critical for the future of society. Public spaces, such as science centers, can impact the communication of science by providing active knowledge-building experiences of scientific phenomena. In contributing to this vision, we have previously developed an interactive visualization as part of a public exhibition about nano. We reflect on how the immersive design and features of the exhibit contribute as a tool for science communication in light of the emerging paradigm of exploranation, and offer some forward-looking perspectives about what this notion has to offer the domain.

Interactive molecular dynamics in virtual reality for accurate flexible protein-ligand docking

Simulating drug binding and unbinding is a challenge, as the rugged energy landscapes that separate bound and unbound states require extensive sampling that consumes significant computational resources. Here, we describe the use of interactive molecular dynamics in virtual reality (iMD-VR) as an accurate low-cost strategy for flexible protein-ligand docking. We outline an experimental protocol which enables expert iMD-VR users to guide ligands into and out of the binding pockets of trypsin, neuraminidase, and HIV-1 protease, and recreate their respective crystallographic protein-ligand binding poses within 5-10 minutes. Following a brief training phase, our studies shown that iMD-VR novices were able to generate unbinding and rebinding pathways on similar timescales as iMD-VR experts, with the majority able to recover binding poses within 2.15 Å RMSD of the crystallographic binding pose. These results indicate that iMD-VR affords sufficient control for users to carry out the detailed atomic manipulations required to dock flexible ligands into dynamic enzyme active sites and recover crystallographic poses, offering an interesting new approach for simulating drug docking and generating binding hypotheses.

Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework

As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often nonintuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline various efforts to extend immersive technologies to the molecular sciences, and we introduce "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application domains where iMD-VR is facilitating research, communication, and creative approaches within the molecular sciences, including training machines to learn potential energy functions, biomolecular conformational sampling, protein-ligand binding, reaction discovery using "on-the-fly" quantum chemistry, and transport dynamics in materials. We touch on iMD-VR's various cognitive and perceptual affordances and outline how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies such as iMD-VR have the potential to improve our ability to understand, engineer, and communicate microscopic dynamical behavior, offering the potential to usher in a new paradigm for engineering molecules and nano-architectures.

Using virtual reality for drug discovery: a promising new outlet for novel leads

Introduction: Virtual reality (VR) environments are increasingly being used by researchers in various fields in addition to being increasingly integrated into various areas of human life, ranging from videogames to different industrial uses. VR can be used to create interactive and multimodal sensory stimuli and thus offers unique advantages over other computer-based approaches for scientific research and molecular-level applications. Consequently, VR is starting to be used in novel drug development, such as in drug discovery, and rational drug design. Areas covered: In this review, the authors discuss the basic development of VR technology, including the available hardware and software. The latest advances of VR technology in novel drug development are then detailed, and the VR programs that can be applied in relevant studies are highlighted. Expert opinion: VR will lead to a revolution in pharmaceutical development. However, there are still obstacles to the successful and extensive application of VR to drug development, including the demand for further improvements to the available hardware and software and the various limitations described with regard to accuracy and precision. As technology continues to improve, the barriers to the widespread adoption of VR will diminish and VR technologies will play an increasingly important role in novel drug development.

Sampling molecular conformations and dynamics in a multiuser virtual reality framework

We describe a framework for interactive molecular dynamics in a multiuser virtual reality (VR) environment, combining rigorous cloud-mounted atomistic physics simulations with commodity VR hardware, which we have made accessible to readers (see isci.itch.io/nsb-imd). It allows users to visualize and sample, with atomic-level precision, the structures and dynamics of complex molecular structures "on the fly" and to interact with other users in the same virtual environment. A series of controlled studies, in which participants were tasked with a range of molecular manipulation goals (threading methane through a nanotube, changing helical screw sense, and tying a protein knot), quantitatively demonstrate that users within the interactive VR environment can complete sophisticated molecular modeling tasks more quickly than they can using conventional interfaces, especially for molecular pathways and structural transitions whose conformational choreographies are intrinsically three-dimensional. This framework should accelerate progress in nanoscale molecular engineering areas including conformational mapping, drug development, synthetic biology, and catalyst design. More broadly, our findings highlight the potential of VR in scientific domains where three-dimensional dynamics matter, spanning research and education.

Multi-scale simulations of biological systems using the OPEP coarse-grained model

Biomolecules are complex machines that are optimized by evolution to properly fulfill or contribute to a variety of biochemical tasks in the cellular environment. Computer simulations based on quantum mechanics and atomistic force fields have been proven to be a powerful microscope for obtaining valuable insights into many biological, physical, and chemical processes. Many interesting phenomena involve, however, a time scale and a number of degrees of freedom, notably if crowding is considered, that cannot be explored at an atomistic resolution. To bridge the gap between reality and simulation, many different advanced computational techniques and coarse-grained (CG) models have been developed. Here, we report some applications of the CG OPEP protein model to amyloid fibril formation, the response of catch-bond proteins to two types of fluid flow, and interactive simulations to fold peptides with well-defined 3D structures or with intrinsic disorder.

Ab initio interactive molecular dynamics on graphical processing units (GPUs)

A virtual molecular modeling kit is developed based on GPU-enabled interactive ab initio molecular dynamics (MD). The code uses the TeraChem and VMD programs with a modified IMD interface. Optimization of the GPU accelerated TeraChem program specifically for small molecular systems is discussed, and a robust multiple time step integrator is employed to accurately integrate strong user-supplied pulling forces. Smooth and responsive visualization techniques are developed to allow interactive manipulation at minimum simulation rates below five MD steps per second. Representative calculations at the Hartree-Fock level of theory are demonstrated for molecular systems containing up to a few dozen atoms.