Fellow’s research: A single domain antibody isolated from Indian camel targets a superbug efflux pump

12 Dec 2019

Fellow’s research: A single domain antibody isolated from Indian camel targets a superbug efflux pump

Dr Aravind Penmatsa, Intermediate Fellow, Indian Institute of Science, Bangalore

In our latest research, we isolated and structurally characterized a unique antibody that targets an efflux pump from Staphylococcus aureus with high affinity.         

Antimicrobial resistance is a huge public health concern today, with the rise of ‘superbugs’ that are resistant to majority of antibiotics. These microbes push out antibiotics from inside the cell through transporters called efflux pumps and thus survive despite the use of antibiotics. Any molecule that detects or blocks efflux pumps could help in identifying drug-resistant microbes and improve the action of antibiotics by blocking their efflux. We designed this study to isolate single-domain antibodies from camels, for use as binders of such efflux pumps in drug resistant pathogens.

Conventionally, antibodies are large proteins (with structural components called heavy chains and light chains) that help in defense against foreign or toxic agents and pathogens. Camelid single-domain antibodies are one-tenth the size of conventional antibodies and lack the light chain. Despite this unusual organization, camelid single-domain antibodies, also called ‘nanobodies’, can bind very tightly to their target antigen. Their shape resembles a rugby ball with long loops that allow interactions with cavities and pockets deep within target protein. These properties improve the ability of these small antibodies to act as blockers of enzymes and inhibitors of substrate transport, with enhanced access to targets compared to antibodies from mice or humans.

We isolated this antibody through a method called yeast surface display screen using cells of a camel immunized with a purified target protein, with help from Dr. Rakesh Ranjan at the National Research Centre on Camel, Bikaner.

Interestingly, the structure of the antibody that we studied has a zinc ion bound in the loop, for stability, instead of a disulfide bond otherwise generally found in single-domain antibodies. Importantly, this antibody targets the efflux pump from extracellular side with high affinity, making it a valuable tool to detect the presence of efflux pumps in pathogenic organisms that play a major role in antimicrobial resistance.

Structure of the metal ion-bound Indian camel antibody

While our study focuses on generating single-domain antibodies against bacterial efflux pumps, this method can also be employed to generate camelid antibodies for use against other biomedical targets. These antibodies can also find use in biotechnological applications that can benefit from their small size and high affinity.


Isolation and structural characterization of a Zn2+-bound single-domain antibody against NorC, a putative multi-drug efflux transporter in bacteria. Sushant Kumar, Mahendran Ithayaraja, Arunabh Athreya, Rakesh Ranjan, and Aravind Penmatsa. Journal of Biological Chemistry. November 2019

Lab webpage: https://aplabmbu.weebly.com

Banner/image credits: Nazia Hussain & Arunabh Athreya