Multiscale Simulation, Modelling and Design



We build computational models that contribute to our understanding of mechanisms of disease and host immune responses, with a particular focus on infective pathogens. Our main method of choice is molecular simulation, using multiscale approaches that allow us to access a broad range of spatio-temporal scales, from atomically-detailed systems to highly simplified coarse-grained resolutions. We interact closely with our numerous experimental collaborators, and develop new ways to integrate diverse structural, biophysical, and biochemical data into models that elucidate biomolecular dynamics and function, and ultimately enable us to work towards novel therapeutic strategies.


Flaviviruses are enveloped viruses which include numerous human pathogens of escalating global health concern that are predominantly transmitted by mosquitoes and ticks. They infect millions of people worldwide each year, exacerbated by ongoing climate changes and globalization. Traditionally, we have focused on the mosquito-borne RNA flavivirus, dengue virus, which represents a significant burden to human health and the economy in Singapore. We have developed “virtual flavivirus” models (Figure 1) that have been used to elucidate key molecular events associated with infection and antibody recognition [1]. For example, we recently studied the phenomenon by which dengue virus particles can switch from a “smooth” to “bumpy” shaped morphology when transmitted from mosquito to human, which we hypothesize can be modulated by mutations thar arise in the envelope protein to evade host immunity by burying vulnerable epitopes. Importantly, we have shown that sufficiently strong antibodies can “outsmart” such adaptations to uncover partially buried epitope sites and neutralize the virus [2]. This shows the importance of selecting high affinity antibodies that can neutralize diverse dengue morphologies in a therapeutic setting. Leveraging on these insights, as part of a collaborative team across Duke-NUS and A*STAR recently funded by an NRF CRP grant, we are pursuing mRNA-based vaccine development to target dengue.


Figure 1. Multiscale modelling of an entire virtual flavivirus (left) provides insights into the viral life cycle and its interactions with host factors such as antibodies, whilst development of a computational platform for the flavivirus envelope raft (right) has enabled atomic-resolution probing for potentially druggable sites on the viral surface.

Some flaviviruses such as dengue exhibit a phenomenon known as antibody-dependent enhancement (ADE), in which a first infection produces antibodies specific against one viral strain, which then imperfectly cross-react with another strain during a subsequent infection. This can complicate traditional vaccinebased approaches to protection against such viruses. As an alternative, the pH-dependent conformational change of the envelope protein required for viral fusion and cellular infection is an attractive point of inhibition by antivirals. To this end, we have recently developed a computational platform to model the flavivirus “raft” as a realistic representation of the viral envelope, enabling probing via drug-like moieties such as benzene to search for hidden, druggable pockets (Figure 1). This approach has been systematically applied to six flaviviral rafts, including dengue, Yellow Fever, and Zika, and revealed a novel, highly conserved cryptic pocket. This pocket was shown to control the pH-sensing mechanism required for fusion and is now being pursued as a potential site for drug targeting and inhibition of the early stages of the viral life cycle [3].


We are leveraging the methods we have developed for flaviviruses to other enveloped viruses including SARS‑CoV‑2, prompted by the COVID-19 pandemic. Supported by an ID HTPO Seed Fund award, we have extensively characterized the structure and dynamics of the SARS-CoV-2 spike protein which covers the pathogen’s surface and is crucial for infection. We have computationally mapped the glycan coating of the spike protein as part of a global collaboration [4-5], showing that constructs derived from different labs are highly similar and closely resemble their viral counterpart. This helps to rationalize the current success of spike-based vaccines targeting SARSCoV- 2 and supports our ongoing surveillance of emerging variants of concern to assess possible effects of mutations upon function or vaccine escape.

At the same time, our computational efforts are providing new functional insights into the spike protein, its role in serious disease, and possible novel therapeutic routes. For example, we discovered with collaborators at BII [6] and NUS [7] that allostery is likely to be vital for both the viral infection process and the emergence of new variants, whilst computational probing of the spike glycoprotein surface has helped us to uncover potentially druggable pockets [8]. As well as being able to bind host factors, in collaboration with researchers at Lund University we have shown that some of these pockets represent high-affinity sites for lipopolysaccharide (LPS) molecules derived from the outer membranes of Gram-negative bacteria [9] (Figure 2). LPS serves as a signal of bacterial infection upon recognition by Tolllike receptor 4 (TLR4) of the innate immune system, but this can also result in over-amplified immune reactions and sepsis. A multidisciplinary approach [10] has elucidated the mechanism by which spike augments hyperinflammation, acting as a conduit in the TLR4 pathway to “boost” innate immune activation (Figure 2). Furthermore, we have extended these studies to also show how LPS can trigger spike protein aggregation in a physiological setting [11]. Collectively, our findings highlight the potential impact of elevated LPS levels in susceptible patients such as those with metabolic disease and Gram-negative bacterial coinfections in severe COVID-19 complications.



Figure 2. Spike protein binds host lipids and metabolites, but also bacterial LPS. In the latter case, it can act as a “conduit”, transferring LPS to the host TLR4 pathway to trigger proinflammatory reactions.


Antimicrobial resistance (AMR) is a leading cause of death worldwide, and there is an urgent need to discover new ways to treat bacterial infections. A multiscale simulation approach can provide an improved understanding of bacterial envelope structure and function [12-13] and contribute towards the development of novel molecules to overcome AMR. We are pursuing a broad range of novel antibacterial therapeutic routes including synthetic cyclic beta-hairpin peptides [14] in collaboration with NUS, endogenous host defence proteins [15] in collaboration with Lund University, and novel classes of antibiotics that interfere with the Gram-negative outer membrane protein assembly machinery [16] in collaboration with the University of Basel. Furthermore, Tuberculosis (TB) kills more people worldwide than any other bacterial infectious disease, and antibiotic resistance is a growing problem affecting its treatment. There has been a recent resurgence of TB drug discovery activities, leading to identification of novel enzyme inhibitors including those that block the essential F-ATP synthase (Figure 3). In collaboration with NTU, we recently elucidated the mechanisms of action of several such inhibitors [17], providing a framework which may potentially be used to develop novel lead compounds that bind to other pathogenic bacterial F-ATP synthases.


Figure 3. The ATP synthase enzyme (left) contains the c-ring turbine (green) whose rotation drives ATP synthesis. The anti-TB drug bedaquiline (BDQ) and its analogues can bind to the c-ring (right) at distinct sites (red, blue, purple) with different affinities and abilities to block catalysis.


 Senior Principal Investigator  BOND Peter J.   |    [View Bio]   
 Senior Scientist I  KRAH Alexander 
 Senior Scientist I MARZINEK Jan
 Senior Scientist I SAMSUDIN Mohd Firdaus 
 Scientist PALUR Venkata Raghuvamsi 
 Scientist SOMBOON Kamolrat
 Scientist MASIREVIC Srdan
 PhD Students DAVIES Thomas Stefan 
 PhD Students WEERAKOON Dhanushka 

Selected Publications

  1. Huber RG, Marzinek JK, Boon PLS, Yue W, Bond PJ. (2021). Computational modelling of flavivirus dynamics: the ins and outs. Methods. 185:28-38.

  2. Fibriansah G, Lim EXY, Marzinek JK, Ng TS, Tan JL, Huber RG, Lim XN, Chew VSY, Kostyuchenko VA, Shi J, Anand GS, Bond PJ, Crowe, Jr. JE, Lok SM. (2021). Antibody affinity versus dengue morphology influences neutralization. PLoS Pathog. 17:e1009331.

  3. Zuzic L, Marzinek JK, Anand GS, Warwicker J, Bond PJ. (2022). A pH-dependent cluster of charges in a conserved cryptic pocket on flaviviral envelopes. bioRxiv. July 13, 2022.

  4. Chawla H, Jossi SE, Faustini SE, Samsudin F, Allen JD, Watanabe Y, Newby ML, Marcial-Juárez E, Lamerton RE, McLellan JS, Bond PJ, Richter AG, Cunningham AF, Crispin M. (2022). Glycosylation and Serological Reactivity of an Expression-enhanced SARS-CoV-2 Viral Spike Mimetic. J Mol Biol. 434:167332.

  5. Allen JD, Chawla H, Samsudin F, Zuzic L, Shivgan AT, Watanabe Y, He WT, Callaghan S, Song G, Yong P, Brouwer PJM, Song Y, Cai Y, Duyvesteyn HME, Malinauskas T, Kint J, Pino P, Wurm MJ, Frank M, Chen B, Stuart DI, Sanders RW, Andrabi R, Burton DR, Li S, Bond PJ*, Crispin M*. (2021). Site-Specific Steric Control of SARS-CoV-2 Spike Glycosylation. Biochemistry. 60:2153-2169.

  6. Tan ZW, Tee WV, Samsudin F, Guarnera E, Bond PJ, Berezovsky IN. (2022). Allosteric perspective on the mutability and druggability of the SARS-CoV-2 Spike protein. Structure. In press.

  7. Raghuvamsi PV, Tulsian NK, Samsudin F, Qian X, Purushotorman K, Yue G, Kozma MM, Hwa WY, Lescar J, Bond PJ, MacAry PA, Anand GS. (2021). SARS-CoV-2 S protein:ACE2 interaction reveals novel allosteric targets. Elife. 17:e1009331.

  8. Zuzic L, Samsudin F, Shivgan AT, Raghuvamsi PV, Marzinek JK, Boags A, Pedebos C, Tulsian NK, Warwicker J, MacAry P, Crispin M, Khalid S, Anand GS, Bond PJ. (2022). Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein. Structure. 30:1062-1074.e4.

  9. Petruk G, Puthia M, Petrlova J, Samsudin F, Strömdahl AC, Cerps S, Uller L, Kjellström S, Bond PJ, Schmidtchen A. (2020)  SARS-CoV-2 Spike protein binds to bacterial lipopolysaccharide and boosts proinflammatory activity. J Mol Cell Biol. 2020 Dec 9:mjaa067. doi: 10.1093/jmcb/mjaa067. Online ahead of print.

  10. Samsudin F, Raghuvamsi P, Petruk G, Puthia M, Petrlova J, MacAry P, Anand GS, Bond PJ, Schmidtchen A. (2022) SARS-CoV-2 spike protein as a bacterial lipopolysaccharide delivery system in an overzealous inflammatory cascade. J Mol Cell Biol. Online ahead of print.

  11. Petrlova J, Samsudin F, Bond PJ, Schmidtchen A. (2022). SARS-CoV-2 spike protein aggregation is triggered by bacterial lipopolysaccharide. FEBS Lett. 596:2566-2575.

  12. Khalid S, Schroeder C, Bond PJ, Duncan AL. (2022). What have molecular simulations contributed to understanding of Gram-negative bacterial cell envelopes? Microbiology. 168:001165.

  13. Tupiņa D, Krah A, Marzinek JK, Zuzic L, Moverley AA, Constantinidou C, Bond PJ. (2022). Bridging the N-terminal and middle domains in FliG of the flagellar rotor. Curr Res Struct Biol. 4:59-67.

  14. Puthia M, Marzinek JK, Petruk G, Ertürk Bergdahl G, Bond PJ, Petrlova J. (2022). Antibacterial and Anti-Inflammatory Effects of Apolipoprotein E. Biomedicines. 10:1430.

  15. Tram NDT, Selvarajan V, Boags A, Mukherjee D, Marzinek JK, Cheng B, Jiang ZC, Goh P, Koh JJ, Teo JWP, Bond PJ, Ee PLR. (2021). Manipulating turn residues on de novo designed β-hairpin peptides for selectivity against drug-resistant bacteria. Acta Biomater. 135:214-224.

  16. Kaur H, Jakob RP, Marzinek JK, Green R, Imai Y, Bolla JR, Agustoni E, Robinson CV, Bond PJ, Lewis K, Maier T, Hiller S. (2021). The antibiotic darobactin mimics a β-strand to inhibit outer membrane insertase. Nature. 593:125-129. 

  17. Krah A, Grüber G, Bond PJ. (2022). Binding properties of the anti-TB drugs bedaquiline and TBAJ-876 to a mycobacterial F-ATP synthase. Curr Res Struct Biol. 4:278-284.