School of biological Sciences

College of Science, NTU, Singapore

A Research Institute Dedicated to Research Excellence in Life Science

School of biological sciences

a Rising star in life sciences

When founded in 2002, the School of Biological Sciences (SBS) had a mission to make

a strong contribution to biological- and biomedical sciences. Since then, many talented

individuals from around the world and Singapore have joined SBS―scientific leaders,

researchers, PhD- and Master students, working in the two divisions of Structural Biology

and Biochemistry as well as Molecular Genetics and Cell Biology. In this publication we

celebrate recent achievements of our scientists in diverse areas such as Peptide Chemistry,

Drug Discovery, Genetics & Disease, Infectious Diseases, Protein Engineering and

Environmental Biotechnology. We hope that you enjoy this first print edition of SBS

Research and that through it you can gain a better picture of the variety of cutting-edge

research being done at SBS.

However, the magazine you are holding is only part of the story. Updated every six

months, SBS Research brings you the very latest research from SBS across a broad

spectrum in life sciences.

We hope all of you will enjoy reading SBS Research and that, over time, this publication

will help to share the entire span of research activities among ourselves, students and

partners in research and in industry.

Prof. M. Featherstone Prof. G. Grüber

Chair of SBS Associate Chair (Research) of SBS

2

Peptide nucleic acid (PNA) is a DNA

mimic with a polyamide backbone. The

high hybridizing affinity and specificity

of PNA has made it an attractive agent for

antigene and antisense research. But poor

cellular uptake is a major disadvantage

that has severely limited its use in

functional genomics and molecular

therapy. The laboratory of A/Prof

Chuan-Fa Liu (SBS, NTU) has designed

a new type of PNA analogue that has

built-in cell-permeability. In this design,

structural moieties with inherent

membrane translocation ability are built

onto PNA’s polyamide backbone without

affecting its hybridization activity. This

is achieved by introducing a guanidine-

bearing peptoid-like side chain onto the

γ-N of the PNA backbone. Thus, this

novel class of nucleic acid mimics

possesses all the desired properties

expected for an ideal antigene or

antisense agent: base-pairing ability, cell-

permeability, in vivo stability and ease of

preparation due to the simplified pseudo-

peptide backbone. The new PNA

analogue will be a useful gene-

knockdown agent both for basic

biomedical research and therapeutic

development.

Cell-permeable Peptide Nucleic Acid

1. Chuan-Fa Liu, Yun Zeng and Xiao-Wei Lu. Peptide Nucleic Acid Monomers and Oligomers. Singapore Patent No.

169162 (date of grant 31 October 2011).

3

Bioactive peptides would be excellent

drug candidates if not for their poor

pharmacokinetic profiles like very short

half-lives in vivo. A major recent

breakthrough is the advent of the so-

called “peptibody” platform technology.

In a peptibody a bioactive peptide of

interest is fused to the Fc domain of

human IgG at either the N- or C-

terminus. A fusion protein so-created has

been shown to have a dramatically

increased half-life that may last for

weeks in an animal’s body. Such

peptide-Fc fusion constructs are

therefore very useful formats for

designing peptide-based drugs, as

validated by the successful development

of the first peptide drug – Nplate®

(romiplostim) – which was discovered

by A/Prof Liu Chuan-Fa (SBS, NTU)

and colleagues while he was at Amgen.

The Peptibody Technology for

Peptide Drug Discovery

1. C.-F Liu, U. Feige, J. C. Cheetham. Thrombopoietic compounds. US Patent #6,835,809 (date of grant 28 Dec. 2004).

4

Peptide Dendrimers As Novel Platform

for Vaccine Development

The laboratory of Prof James P. Tam

(SBS, NTU) invented a new technological

platform known as multiple antigen

peptides (MAP) or peptide dendrimers for

development of safe and effective vaccines.

In the MAP system, multiple copies of

antigenic peptides are bound to a non-

immunogenic Lys-based dendritic scaffold.

The MAP molecules acquire proteolytic

stability, enhanced molecular recognition

by immune cells, and induction of stronger

immune responses compared with

monomeric peptides. This structure permits

controlled structure-activity relationship

studies, and is applicable for oral or nasal

delivery to elicit mucosal immune

responses. The MAP-based vaccines also

eliminate the need for the inclusion of

adjuvants found to be toxic to humans, and

avoid the adverse effects associated with

conventional vaccines (i.e., live-attenuated,

killed or inactivated pathogens), carrier

proteins and cytotoxic adjuvants.

Since the introduction of MAPs by Tam’s

research group, over 200 applications of

MAPs have been documented in the

literature. It has become a popular method

with many vaccines currently being studied

in clinical trials in the treatment for

malaria, influenza, tuberculosis and HIV.

Commercial companies specializing in

peptide reagents now offer either reagents

for synthesizing MAPs in the laboratory or

by custom synthesis services.

1. U.S. and Denmark Patents no. 398,846: A Method for Rapid and Multiple Peptide Synthesis.

2. WO Patent no. 011778: Dendritic Polymer of Multiple Antigen Peptide System Useful as Anti-Malarial Vaccine.

3. WO Patent no. 003766: Multiple Antigen Peptides for Use as HIV Vaccines.

4. U.S. Patent no. 5,580,563: Multiple antigen peptide system having adjuvant properties, vaccines prepared therefrom and

methods of use thereof.

5. U.S. Patent no. 5,229,490: Multiple antigen peptide system

5

Genetic manipulation of genomes is an important

component of many applications in biotechnology

and molecular medicine. Prominent examples

include generation of genetically modified cells for

the production of protein therapeutics/diagnostics,

drug testing/development and gene therapy.

However, existing gene insertion technologies

often lack desired target sequence specificity and

are mostly irreversible. These features can result in

potentially harmful genomic mutations and/or

unpredictable complications. The laboratory of

A/Prof Peter Dröge (SBS) possesses a patented,

site-specific genome insertion technology which

has found commercial application. It enables users

to express any transgenic DNA construct of

interest from a pre-determined, single genomic

docking site. Examples of potential applications of

this technology, in particular in conjunction with

our novel “in-house”-developed embryonic stem

cell pluripotency reporter system, include GMO

production, gene therapy, and drug screening.

Genome surgery for biotechnological

and medical application

1. Dröge, P. Sequenz-spezifische Rekombination in eukaryotischen Zellen. Patent granted in China (2004), Australia (2005)

Mexico (2006), Korea (2005) European Union (2006), Israel (2008), India (2009), Singapore (2008)

2. Dröge, P., Enenkel, B. (2002): Sequenz-specific recombination in eukaryotic cells.

3. Liu, A. O, Liang, X. J., Zhang, X. M. Sun, S, Drőge, P. (2009): Microfluidic Cell Sorter System.

4. Ghadessy, F. J., Sian,T. M., Drőge, P. (2009): Muteins of the Bacteriophage λ Integrase. PCT in 2011

6

A novel process and reagents for rapid

genetic alterations in eukaryotic cells

1. Makeyev E.V., Khandelia P., Yap K. (2011) A novel process and reagents for rapid genetic alterations in eukaryotic cells.

US Provisional Patent Application No.: 61/504,577.

2. Khandelia P., Yap K., Makeyev E.V. (2011) Streamlined platform for short hairpin RNA interference and transgenesis in

cultured mammalian cells. Proc. Natl. Acad. Sci. USA 108, 12799-12804.

3. Dai W., Zhang G., Makeyev E.V. (2012) RNA-binding protein HuR autoregulates its expression by promoting alternative

polyadenylation site usage. Nucleic Acids Res. 40, 787-800.

Sequence-specific gene silencing by short hairpin (sh) RNAs has recently emerged as an

indispensable tool for understanding gene function and a promising avenue for disease

therapies. However, a wider biomedical use of this approach is hindered by the lack of

straightforward methods for achieving uniform expression of shRNAs in mammalian cell

cultures. To this end, the group of Asst Prof Eugene Makeyev (SBS, NTU) has developed

a high-efficiency and low-background (HILO) recombination-mediated cassette exchange

(RMCE) technology that yields virtually homogeneous cell pools containing doxycycline-

inducible shRNA elements in a matter of days and with minimal efforts (1, 2). The utility

of this approach has been shown for a number of commonly used human and mouse cell

lines. Because of its technical simplicity and cost efficiency, the technology should

facilitate both low- and high-throughput shRNA-based RNA interference projects.

Moreover, a recent study by the Makeyev lab demonstrates (3) that HILO-RMCE will be

useful for a wider range of molecular and cell biology applications by allowing one to

rapidly engineer cell populations expressing essentially any transgene of interest.

7

The cyclic dinucleotides c-di-GMP and c-

di-AMP are newly discovered bacterial

messenger molecules with potent

immunostimulatory properties. With their

potential to be used as immunologic or vaccine

adjuvants, efficient synthesis of the

dinucleotides in large quantity is essential for

research and clinical trial purposes. Currently,

c-di-GMP and c-di-AMP can be obtained by

multi-step chemical synthesis methods that are

not suitable for large scale production.

Enzymatic synthesis of c-di-GMP using

mesophilic enzymes suffers from low

production yield due to protein instability and

strong product inhibition. The laboratory of

A/Prof Zhao-Xun Liang (SBS, NTU) lab has

cloned and engineered two hyperthermophilic

enzymes: a diguanylate cyclase (tDGC) and a

diadenylate cyclase (tDAC), for the enzymatic

synthesis of c-di-GMP and c-di-AMP. The

product inhibition that previously limited

production yield of c-di-GMP was

significantly alleviated by protein engineering

in the putative regulatory inhibition site. With

the engineered enzymes, the lab demonstrated

that grams of c-di-GMP/AMP can be readily

prepared by using the procedures optimized

for enzymatic reaction and product

purification. The thermophilic enzymes are not

only highly valuable for large-scale c-di-

GMP/AMP production but also suitable for the

preparation of radioisotope-labeled c-di-

GMP/AMP derivatives.

Enzymatic Synthesis of Cyclic Dinucleotides

as Potent Immunostimulatory Agents

1. Liang, Z.-X., Rao, F. (2010) Engineering of a thermophilic diguanylate cyclase for large-scale production of cyclic-di-GMP.

US Patent 1/156/826.

2. Liang, Z.-X., Pasunooti, S. (2011) Efficient enzymatic synthesis of cyclic and linear diadenosine monophosphates by thermophilic

enzymes. US Patent application No. PCT/SG2010/000060.

8

Proteolytic peptides as biomarkers for

hemoglobinopathies and other diseases

1. Tang, K., Sanmun, D., Fucharoen, S., Law, H. Y., Ng, I. (2011) Proteolytic peptides as biomarkers for thalassemia and other

genetic diseases, US provisional patent filed (#61/491,489).

Protein biomarker discovery efforts are usually

hampered by the fact that most of the candidate

markers identified result from the body’s

response to diseases, rather than disease-causing

proteins themselves. This often raises serious

questions about the specificity of these candidate

markers. On the other hand, disease-causing

protein mutations, if known and easily detected,

could serve as ultimate biomarkers. However,

proteins carrying such mutations are rare and

often in low abundance, making them difficult to

be detected. The laboratory of Asst. Prof Kai

Tang (SBS, NTU) hypothesized that these

proteins are degraded by endogenous proteases

and the proteolytic peptides carrying the

mutation could be more readily detected and

serve as potential biomarkers for diseases. They

tested this hypothesis in α-thalassemia patients

with stop-codon mutations and identified a

number of proteolytic peptides. The sequence of

these peptides matched with the C-terminal

fragments of the elongated α-globin. They have

been identified in peripheral blood carrying the

Hb CS (Hb Constant Spring) or PS (Pakse)

allele, including homozygotes and heterocygotes The researchers also found that in samples carrying HbE allele, a common Hb variant in

Southeast Asia due to mutation in beta globin chain, proteolytic peptides carrying the HbE

mutation could also be found in peripheral blood of both homozygous and heterozygous

carriers. Furthermore, proteolytic peptides from sickle cell samples carrying specific

mutations HbS and HbC can also be found in peripheral blood. When validated, the

method can be used for high-throughput screening of hemoglobinopaties or other diseases

using tandem mass spectrometry.

b a

X

a-thalassemia

9

Antibody as a potential component

of Blocking invasion in Malaria

1. Gao, X., Preiser, P. R. Binding Domain of Plasmodium Reticulocyte Binding Proteins. Singapore Patent No. 150149 (date of

grant 8 December 2011)

2. Gao, X. Preiser, P. R. (2008) Antibodies targeting the PfRH1 binding domain inhibit invasion of Plasmodium falciparum

merozoites. PLoS Pathog. 4, e1000104

Invasion by the malaria merozoite

depends on recognition of specific

erythrocyte surface receptors by parasite

ligands. Plasmodium falciparum uses

multiple ligands, including the

reticulocyte binding protein homologues

(RHs). RH are conserved in all species

of Plasmodium and play an important

role in host cell sensing and recognition

as well as virulence. The group of Prof

Peter Preiser (SBS, NTU) has identified

the functional region of RH proteins that

mediates the initial binding of the

protein to a specific receptor on the

erythrocyte surface. Antibodies against

this domain are able to block invasion of

the merozoite efficiently. The relatively

small (334 amino acid) region of RH that

encodes the binding domain is ideal for

recombinant protein expression and can

serve as a potential component of an

invasion blocking antibody.

Invasion

10

Bacterial Co-cultures as tools in

Environmental Biotechnology

The concept of Bioaugmentation in

Environmental Biotechnology is not new –

this involves adding microbial strains with

specialized ability, e.g. degradation of toxic

pollutants, to the site where the specific

function is needed. However, applying a

single strain has often proven ineffective.

Asst Prof Sze Chun Chau’s laboratory

(SBS, NTU) explores and exploits bacterial

interplay in order to achieve a more

sophisticated level of Bioaugmentation.

Interactions between various bacterial

species bring about differing outcomes. A

compatible combination of bacterial

species, with complementary and

synergistic metabolic capabilities, can result

in a potent co-culture suitable for handling

applications not possible with pure cultures.

One of the greatest advantage of bacterial

co-cultures over pure cultures is that co-

cultures are often more resistant to

environmental disturbances and fluctuation,

and hence, more self-sustaining. This work

has benefitted our industry partners in the

Environmental Biotechnology sector, e.g.

an air-purification device for removing

Volatile Organic Compound (VOC) will be

making use of the bacterial co-culture

formulated by Asst Prof Sze’s laboratory,

which can remove VOC more than 400%

faster, compared to their original version.

Licensing terms are being negotiated

currently.

11

1. Hansen, J. S., Vararattanavech, A., Plascencia, I., Greisen, P. J., Bomholt, J. Torres, J. Emneus, J., Helix-Nielsen, C.

(2011) Interaction between sodium dodecyl sulfate and membrane reconstituted aquaporins: a comparative study of

spinach SoPIP2;1 and E. coli AqpZ (2011) BBA –Biomembranes, 1808, 2600-2607.

2. Jesper S. Hansen, A. Vararattanavech, T. Vissing, J. Torres, J. Emnéus, C.H. Nielsen (2011) Formation of giant protein

vesicles by a lipid cosolvent method. ChemBioChem 12, 2856-2862.

The laboratory of A/Prof Jaume Torres (SBS,

NTU) developed together with Aquaporin A/S

(Denmark) a method to create giant protein vesicles

(GPVs). Fluorescence microscopy is used to

characterize GPV morphology and protein–lipid

hydrophobic interactions. Specifically, they

employed generalized polarization imaging to

monitor the polarity around the protein

transmembrane region of aquaporins labeled with the

polarity-sensitive probe Badan.

Their recently published work (1,2), describes how

giant protein vesicles (GPVs) of ≥10 μm can be

created by solvent-driven fusion of large vesicles

(0.1-0.2 μm) with reconstituted membrane proteins.

The researchers found that formation of GPVs

proceeded from rotational mixing of protein-

reconstituted large unilamellar vesicles (LUVs) with

a lipid-containing solvent phase. GPVs can be made

by using n-decane and squalene as solvents, and

applied generalized polarization (GP) imaging to

monitor the polarity around the protein

transmembrane region of aquaporins labeled with the

polarity-sensitive probe Badan. Specifically, they

created GPVs of spinach SoPIP2;1 and E. coli AqpZ

aquaporins. There findings show that hydrophobic

interactions within the bilayer of formed GPVs are

influenced not only by the solvent partitioning

propensity, but also by lipid composition and

membrane protein isoform.

Polarity exploration

12

Together with the NS5 polymerase, the

NS3 helicase has a pivotal function in

flavivirus RNA replication and constitutes an

important drug target. The laboratory of

A/Prof Julien Lescar (SBS, NTU) and the

Novartis Institute for Tropical Diseases

(Singapore) captured the dengue virus NS3

helicase at several stages along the catalytic

pathway including the forms bound to

single-stranded (ss) RNA, to an ATP

analogue, to a transition-state analogue and

to ATP hydrolysis products. RNA

recognition appears largely sequence

independent in a way remarkably similar to

eukaryotic DEAD box proteins Vasa and

eIF4AIII. On ssRNA binding, the NS3

enzyme switches to a catalytic- competent

state imparted by an inward movement of the

P-loop, interdomain closure and a change in

the divalent metal coordination shell,

providing a structural basis for RNA-

stimulated ATP hydrolysis. These structures

demonstrate for the first time large

quaternary changes in the flaviviridae

helicase, identify the catalytic water

molecule and point to a β-hairpin that

protrudes from subdomain 2, as a critical

element for dsRNA unwinding. They also

suggest how NS3 could exert an effect as an

RNA-ancho ring device and thus participate

both in flavivirus RNA replication and

assembly.

Insights into RNA unwinding and

ATP hydrolysis by the flavivirus NS3 protein

1. Luo, D., Xu, T., Watson, R. P., Scherer-Becker, D., Sampath, A., Jahnke, W., Yeong, S. S., Wang, C. H., Lim, S. P., Strongin,

A.,Vasudevan, S. G., Lescar, J. (2008) EMBO J. 27, 3209–3219

13

Functional analysis of two cavities

in flavivirus NS5 polymerase

1. Zou G., Chen Y. L., Dong H., Lim C. C., Yap L. J., Yau Y. H., Shochat S. G., Lescar J., Shi P. Y. (2011) J. Biol. Chem. 286,

14362-14372. (2011) J. Biol. Chem. 286, 14362-14372

Flavivirus NS5 protein encodes

methyltransferase and RNA-dependent RNA

polymerase (RdRp) activities. Structural analysis

of flavivirus RdRp domains uncovered two

conserved cavities (A and B). Both cavities are

located in the thumb subdomains and represent

potential targets for development of allosteric

inhibitors. The laboratory of A/Prof Susana

Geifman Shochat (SBS, NTU) analyzed in

collaboration with the Novartis Institute for

Tropical Diseases (Singapore) the function of

the two RdRp cavities. Amino acids from both

cavities were subjected to mutagenesis analysis

in the context of genome-length RNA and

recombinant NS5 protein; residues critical for

viral replication were subjected to revertant

analysis. For cavity A, they found that only one

(Lys-756) of the seven selected amino acids is

critical for viral replication. Alanine substitution

of Lys-756 did not affect the RdRp activity,

suggesting that this residue functions through a

nonenzymatic mechanism. For cavity B, all four

selected amino acids (Leu-328, Lys-330, Trp-

859, and Ile-863) are critical for viral

replication. Biochemical and revertant analyses

showed that three of the four mutated residues

(Leu-328, Trp-859, and Ile-863) function at the

step of initiation of RNA synthesis, whereas the

fourth residue (Lys-330) functions by interacting

with the viral NS3 helicase domain. Collectively,

their results have provided direct evidence for

the hypothesis that cavity B, but not cavity A,

from dengue virus NS5 polymerase could be a

target for rational drug design.

14

Important Role for Heat Shock Protein 90

in Virus Particle Assembly

1. Radhakrishnan, A., Yeo, D., Brown, G., Myaing, M. Z., Iyer, L. R., Fleck, R., Tan, B.-H., Aitken, J., Sanmun, D., Tang, K.,

Yarwood, A., Brink, J., Sugrue, R. J. (2010) Molecular & Cellular Proteomics 9:1829–1848

The laboratory of A/Prof Richard

Sugrue (SBS, NTU) and researchers of

JEOL U.S.A. Inc., (Massachusetts)

identified the presence of virus-associated

cellular proteins that may play a role in

respiratory syncytial virus (RSV)

maturation. Fluorescence microscopy of

virus-infected cells revealed the presence

of virus-induced cytoplasmic inclusion

bodies and mature virus particles, the

latter appearing as virus filaments. In situ

electron tomography suggested that the

virus filaments were complex structures

that were able to package multiple copies

of the virus genome. The virus particles

were purified, and the protein content was

analyzed by one-dimensional nano-LC

MS/MS. In addition to all the major virus

structural proteins, 25 cellular proteins

were also detected, including proteins

associated with the cortical actin network,

energy pathways, and heat shock proteins

(HSP70, HSC70, and HSP90).

Immunofluorescence microscopy of infected cells stained with antibodies against

relevant virus and cellular proteins confirmed the presence of these cellular proteins in

the virus filaments and inclusion bodies. The relevance of HSP90 to virus infection

was examined using the specific inhibitors 17-N-Allylamino-17-

demethoxygeldanamycin. Although virus protein expression was largely unaffected by

these drugs, we noted that the formation of virus particles was inhibited, and virus

transmission was impaired, suggesting an important role for HSP90 in virus

maturation. This study highlights the utility of proteomics in facilitating both our

understanding of the role that cellular proteins play during RSV maturation and, by

extrapolation, the identification of new potential targets for antiviral therapy.

15

Crystal structure analysis of Flavivirus

methyltransferases uncovered a

flavivirus-conserved cavity located next

to the binding site for its cofactor, S-

adenosyl-methionine (SAM). Chemical

derivatization of S-adenosyl-

homocysteine (SAH), the product

inhibitor of the methylation reaction, with

substituents that extend into the identified

cavity, generated in- hibitors that showed

improved and selective activity against

dengue virus methyltransferase (MTase),

but not related human enzymes. The

crystal structure of dengue virus MTase

with a bound SAH derivative, solved by

the laboratory of A/Prof Julien Lescar

(SBS, NTU) and the Novartis Institute

for Tropical Diseases (Singapore),

revealed that its N6-substituent bound in

this cavity and induced conformation

changes in residues lining the pocket.

These findings demonstrate that one of

the major hurdles for the development of

methyltransferase-based therapeutics,

namely selectivity for disease-related

methyl- transferases, can be overcome.

Small Molecule Inhibitors That

Selectively Block Dengue

1. Lim, S. P., Sonntag, L. S., Noble, C., Nilar, S. H., Ng, R. H., Zou, G., Monaghan, P., Chung, K. Y., Dong, H., Liu, B.,

Bodenreider, C., Lee, G., Ding, M., Chan, W. L., Wang, G., Jian, Y. L., Chao, A. T, Lescar, J., Yin, Z., Vedananda, T. R.

Keller, T. H., Shi, P.Y. (2011) J. Biol.Chem. 286, 6233–6240

16

a novel mechanism of inhibition

of the TB drug TMC207

1. Biuković, G., Basak, S., Manimekalai, M. S. S., Rishikesan, S., Roessle, M, Dick, T., Rao, S. P. S, Grüber, G. (2012) Variations of subunit of the Mycobacterium tuberculosis F-ATPsynthase and a novel mechanism of inhibition of the TB drug TMC207. PNAS

With one-third of mankind infected

subclinically, and an incidence of nine

million new cases of active tuberculosis

disease (TB) and two million deaths per

year, Mycobacterium tuberculosis

remains the most important bacterial

pathogens in the world. TMC207 was

identified in a phenotypic whole cell

screen and described to interfere with the

M. tuberculosis F-ATP synthase.

Using NMR-, SAXS, fluorescence

spectroscopy and mutagenesis, the

laboratory of Prof Gerhard Grüber

(SBS, NTU) in collaboration with the

Novartis Institute for Tropical Diseases

(Singapore) demonstrated that the new

TB drug candidate TMC207, proposed to

bind to the proton translocating c-ring,

also bind to the coupling subunit ε of the

M. tuberculosis F-ATP synthase. The data

demonstrate that TMC207 forms a wedge

between the two rotating subunits c and ε

by interacting with the residues W15 and

F50 of ε and the c-ring, respectively. T19

and R37 of ε provide the necessary polar

interactions with the drug molecule. This

new mechanism of TMC207 binding

provides the basis for the design of

antimycobacterials, targeting the F-ATP

synthase in M. tuberculosis.

17

Bactericidal Boomerangs

1. Bhunia, A., Mohanram, H., Domadia, P. N., Torres, J., Bhattacharjya, S. (2009) Designed beta-boomerang antiendotoxic and

antimicrobial peptides:structures and activities in lipopolysaccharide. J. Biol. Chem. 284, 21991-22004

Lipopolysaccharide (LPS), a major

component of the outer membrane of

Gram-negative bacteria, is perhaps best

recognized as a potent inducer of the

innate immune system. However, LPS

also acts as a barrier to exogenous

compounds and a chaperone to aid in the

folding of outer membrane proteins.

Therefore, molecular interactions with

LPS should be considered when

designing antimicrobial drugs. Dr. Surajit

Bhattacharjya and colleagues (SBS,

NTU) do just that, describing structure

activity correlations for a series of 12-

residue peptides (based on chemokines

and neutrophil bactericides) in LPS. They

observed that long range aromatic-

aromatic packing between residues

located at positions 4 and 9 (forming a

boomerang-like conformation) was

crucial for both neutralizing LPS and

antimicrobial activity; the ability of these

active peptides to neutralize LPS

appeared to correlate with their ability to

perturb LPS micelles. This atomic level

knowledge should be useful in providing

the building blocks for designing novel

peptides for bacterial outer membranes.

18