Multiscale Simulation, Modelling, and Design

Peter J. BOND
Principal Investigator

Daniel A. HOLDBROOK*, Roland G. HUBER, Jan K. MARZINEK Postdoctoral Scientists

Alister T. BOAGS, Priscilla BOON, Eilish W. MCBURNIE, Aishwary T. SHIVGAN*, Samantha L. WEETMAN, Lorena ZUZIC PhD Students

* Co-supervised with Chandra Verma

The group uses computational modelling and simulation to understand the function of biomolecular systems over multiple time and length scales. We are particularly interested in molecular mechanisms of infectious disease, the host response to pathogens such as viruses and bacteria, and ultimately, therapeutic intervention strategies. The methodological foundations of our research are rooted in the combination of computation and experiment; we interact closely with our many collaborators, working towards integrative structural models with which we formulate and test new hypotheses. Our approach encompasses several "flavours" of simulation, ranging from rigorous atomic-resolution sampling methods, to hierarchical coarse-grained representations of realistic multi-component systems. Collectively, this combination of techniques serves to enhance the nature and breadth of the biological insights we can access.

Multiscale Dynamics of Pathogenic Viruses

A major focus of the group's research is on understanding the mechanisms of host cell recognition and invasion by flaviviruses such as dengue and Zika. Such pathogens infect millions of people worldwide each year, and represent a major, ongoing health threat in Singapore. As part of an MOE-funded, Singapore-wide collaborative team of fourteen researchers, including Chandra Verma here at BII and experimentalists at NUS, NTU, and Duke-NUS, we have been unravelling the details of the infective viral life cycle. As reviewed in [16], we have achieved this using integrative modelling and simulation over multiple spatiotemporal scales, ultimately working towards therapeutics discovery. The virus particle is known to be like an onion; the outermost layer is made up of a lipid/protein envelope complex, which in turn encapsulates the core containing the genetic information of the virus. Since structural details for the complete virion are missing, we have been developing new approaches to model in near-atomic detail the flaviviral lipid shell, in close accordance with biophysical experiments, and the genomic core, guided by next-generation sequencing approaches supported by our colleagues at GIS (A*STAR) and the University of Lisbon. Our "virtual virus" has helped to establish details of its "breathing" dynamics, which arthropod-borne viruses may use to "sense" changes in environment upon transfer to the human host, triggering the infective process. Further along the life cycle, we have constructed integrative structural models for the "spiky" form of dengue, enabling observation of viral fusion with intracellular host membranes (Figure 1), prior to injection of the viral genetic material into the cytoplasm. In parallel, we are investigating how such viruses interact with cell surface receptors and antibodies during both maturation and infection, helping us to search for new druggable sites, as well as to block such interactions with synthetic compounds developed by researchers at BTI ( A*STAR). We have also worked closely with Sebastian Maurer-Stroh at BII to combine structural models with bioinformatics approaches, to e.g. identify potential virus components for use in diagnostic testing [14]. Most recently, we were awarded an NRF-funded grant with workers at NUS, SGH, Duke-NUS, and SIgN (A*STAR), to leverage on our significant process in understanding the dynamics of enveloped viruses and develop novel approaches to the targeted discovery of novel antibodies and vaccines.

^ Figure 1: Simulation of a fusogenic dengue virus particle.
In (A), the "spiky" virus is interacting with a host endosomal membrane, and (B) shows the latter stages of membrane fusion.

Mechanisms of Bacterial Infection and Host Defense

Bacteria represent a significant threat to human health, particularly given the imminent global crisis of multidrug resistance. The envelopes of Gram-negative bacteria such as E. coli contain lipopolysaccharide (LPS) molecules on their surface, which make the associated outer membrane robust and highly impermeable to toxins and antibiotics, whilst stabilizing protein machinery which serve functional roles in e.g. nutrient transport, virulence, and toxin secretion (Figure 2). An improved understanding of the structure and dynamics of bacterial membranes would help in the search for novel approaches to antimicrobial therapy. As reviewed in [11], with researchers at the University of Southampton we have developed the most realistic models to date of the bacterial envelope, enabling us to identify potential points of weakness that may be targeted by drugs or peptides to disrupt the protective outer layer of bacterial cells. Furthermore, by integrating biochemical data from collaborators at the Life Sciences Institute (NUS) with multiscale simulations, we have gained important insights into how bacteria maintain the asymmetric lipid composition of their outer membranes whilst preserving the impermeability that is crucial to their survival and pathogenesis [4]. Furthermore, a variety of integrative modelling projects, combining diverse experimental data including crystallography, NMR, small-angle X-ray scattering, and cryo-electron microscopy, with collaborators spanning the University of Manchester, Biozentrum Basel, and Pasteur Institute, have provided exciting new insights into the biogenesis and secretory modes of bacterial envelope LPS [13] and toxins [12], including the dynamic mechanism of a chaperone essential to the folding and insertion of bacterial outer membrane proteins [10] (Figure 2).

LPS also signals the presence of a bacterial infection to the mammalian innate immune response, via the Toll-like receptor 4 (TLR4) system. This is of great therapeutic interest, in light of the potential to manipulate this pathway in new vaccine formulations, and because overstimulation of the pathway by excessive bacterial LPS "endotoxin" can lead to sepsis, a leading worldwide cause of mortality. Building on our earlier work (see e.g. [11]), we have developed multiscale models for the TLR4 pathway [5,7], enabling us to trace the complete endotoxin cascade, from LPS extraction at the bacterial envelope to recognition by terminal receptor complexes at the host cell surface (Figure 2). Such models again benefit from a wide collaborative network spanning Cambridge University, the Baker IDI Heart and Diabetes Institute (Melbourne) and the University of Colorado, and provide important new insights into mechanisms of disease [1,2], such as dietary fatty-acid induced metabolic disease and the inflammatory potential of gut microbiota. Most recently, in collaboration with Artur Schmidtchen and co-workers (LKCMedicine and Lund University), we have integrated a range of information derived from biophysical and cellular biology with this "multiscale endotoxin platform" to uncover several novel host defense mechanisms. These are associated with essential control of endotoxins and bacteria during wound healing, and could be leveraged to develop new ways to fight infections. Thus, naturally occurring peptides cleaved from thrombin during blood clotting were shown to serve functions in the neutralization of microbes, by forming amyloid-like aggregates with LPS and bacteria, facilitating cell permeabilization and phagocytic uptake [9]. Other thrombin-derived peptides were also discovered to have dual antimicrobial and antisepsis activity, helping to scavenge LPS molecules and aggregates as well as potentially inhibiting and hence down-regulating receptors in the TLR4 pathway [3] (Figure 2).

Novel antimicrobials against resistant bacteria
^ Figure 2: Bacterial membranes and host defense.
(A) Periplasmic chaperone Skp bound to an outer membrane protein, prior to its folding and insertion into a bacterial outer membrane containing LPS, depicted in (B). In (C), the CD14 coreceptor of the TLR4 pathway is shown bound to an endotoxic bacterial LPS molecule (left) or to a peptide naturally derived from thrombin during the blood clotting cascade in wounds (right).

Multiscale Simulation, Modelling, and Design Members

Dr. Peter J. Bond
Principal Investigator
  Biography Details
Dr. BOND Peter JohnPrincipal Investigator
Dr. HOLDBROOK DanielPostdoctoral Fellow
Dr. HUBER RolandPostdoctoral Fellow
Dr. MARZINEK JanPostdoctoral Fellow
Ms. BOON Li Shan Priscilla PhD student
Mr. SHIVGAN Aishwary Tukaram PhD student
Ms. WEETMAN Samantha PhD student
Ms. Alister BOAGS PhD student
Ms. Lorena ZUZIC PhD student
Mr. Dale Stuchfield * PhD student

This section is still work in progress.