Basu Lab


Research Focus

“Emerging infections” have been defined as infections that have either newly appeared, or that have appeared previously but are expanding in incidence and geographic range, or that threaten to increase in the near future. Emerging viral diseases have threatened humanity throughout history. Changes in ecology – whether they are a result of deforestation, enhanced global transportation and commerce, or practices within a hospital—have accelerated both the emergence and spread of viruses. Sometimes outbreaks occur and then fizzle out as happened with the SARS coronavirus in 2003, while other times novel virus strains circulate globally, as occurred in the 2009 influenza pandemic or 2013-2015 Ebola pandemic. Viruses, especially the RNA viruses, can quickly adapt to and exploit these varying conditions because of the high error rates of the viral polymerases that replicate their genomes. Therefore, it comes as no surprise that the majority of the recent examples of emerging or re-emerging diseases are caused by RNA viruses. My laboratory is interested in understanding the mechanisms of viral pathogenesis at the molecular level and using this knowledge for developing new antiviral drugs. The research involves basic molecular biology and virology techniques combined with RNAi, proteomics and high-throughput screening of small molecular weight compounds.

Influenza A virus:

Fig.1. Influenza Virus minigenome assay

Influenza A virus is a classic example of emerging viral infection. The viral strains are responsible for seasonal epidemics and have caused the three pandemics in the 20th century (1918, 1957 and 1968) as well as the 2009 H1N1 pandemic. Wild aquatic birds are the natural reservoir of Influenza A viruses. Pandemics occur when a “new influenza virus” emerges, due to antigenic ‘shift’, to which the human population is immunologically naive. The neuraminidase (NA) inhibitor, oseltamivir, is the cornerstone for response plans to a future influenza A virus epidemic and/or pandemic. However, the emergence of oseltamivir resistant A/H1N1, A/H3N2 and A/H5N1 influenza strains raises a major concern for public health and underlines the need for new and effective antiviral therapy.


Targeting Viral Polymerase

Our laboratory in collaboration with other groups at Southern Research is using a Discovery Chemical Biology approach to develop new antivirals and to study viral replication and their cellular processes using the plasmid-driven minigenome assay (or minireplicon assay) developed at the laboratory of Dr. Peter Palese at The Icahn School of Medicine at Mount Sinai, New York. This assay is a powerful cell-based assay to study influenza virus polymerase and the host factors that help in its replication. It relies on expression from plasmids of polymerase subunits PB1, PB2, and PA, NP, and a virus-like minigenome RNA molecule of negative polarity containing a reporter gene (for example, a luciferase, in our case), mimicking a viral genomic segment (Figure 1). Expression of the reporter gene is an indirect measure of the activity of the reconstituted influenza virus polymerase. The virus-like minigenome is transcribed from the reporter plasmid by the cellular

RNA polymerase I (Pol I), whose promoter sequence is species-specific. Using this minigenome assay and other molecular biology assays we have identified several compounds that inhibit influenza polymerase. We are now working to optimize these compounds in collaboration with other laboratories and characterize how these compounds inhibit viral replication.


Inhibition of Host Innate Immune Pathways by Influenza Virus:

Another focus of our laboratory is the host antiviral response and specifically the mechanisms that influenza virus use to block this response. The Non Structural 1 (NS1) protein of influenza virus is a 230–237 amino acid multifunctional protein, one of whose actions is to antagonize the interferon response. It contains an RNA binding domain (RBD) that is relatively well-conserved among different strains and a variable effector domain (ED) that is connected by a linker. One druggable function of NS1 is its IFN-antagonist activity, as this is essential for efficient virus replication and for lethality in vivo. The RBD domain of NS1 sequesters the viral RNA protein and inhibits IFNα/β production by inhibiting the RIG-I signaling pathway, which triggers synthesis of the antiviral cytokines IFNα/β in response to viral nucleic acids. Viral proteins such as NS1 that can inhibit the host innate immune response are important determinants of viral pathogenicity. Understanding their mechanism of action and identifying compounds that prevent their activity will aid in the design of attenuated viruses for vaccine purposes or in the discovery of new antiviral drugs. We are developing cell-based (Figure 2) assays to identify compounds that will prevent the virus to escape innate immune response.

Study of Viral Entry

The viral envelope glycoprotein orchestrates entry of the virus into its target cell by mediating attachment to cell-surface receptors and fusion of the virus and cell membranes. My laboratory is interested in cellular, molecular, and structural aspects of virus entry of several important emerging viruses namely Ebola (EBOV), Marburg (MARV) virus and Zika virus (ZIKV).


EBOV and MARV viruses cause highly lethal viral hemorrhagic fever syndrome. The recent 2013-2015 Ebola epidemic in West Africa shows the global challenge of dealing with this deadly pathogen. One of the key questions in our understanding of filoviral biology, the entry mechanism of these viruses, is still poorly understood. Entry of filovirus into the hosts is mediated by a single viral glycoprotein (GP), which consists of two subunits, GP1 and GP2, linked together by a disulfide bond. GP1 is responsible for receptor binding and host tropism, while GP2 mediates viral/cell membrane fusion and viral entry. Using various surrogate models and working collaboratively with our collaborators, we are working to identify critical host factors required for cell infection by EBOV. Our focus is to decipher how host-encoded factors can influence the susceptibility of humans and animals to viral infection. Our ongoing efforts also include translational studies to develop anti-Ebola drugs, including small molecule and antibody therapeutics, targeting viral and host factors critical for infection.


The mosquito-borne ZIKV has recently emerged as a major global health threat, in part due to its apparent association with clinical microcephaly in babies born to infected mothers. ZIKV infection has also been associated with severe neurological sequelae such as Guillain-Barre syndrome in infected patients. Despite its global public health burden, there is no clinically approved therapy for ZIKV infection. To address this huge unmet medical need, we take a multidisciplinary approach (i) to study the molecular mechanism of viral entry and (ii) to translate the knowledge into antivirals, vaccine, and diagnostic products.

The goal of my laboratory is to understand the mechanisms of viral pathogenesis associated with emerging virus infection, and use this information to develop therapeutic protocols and vaccines that will confer long-term protective immunity.


Arnab Basu, Ph.D.

Associate Fellow, Infectious Diseases Department

Arnab Basu, Ph.D., is an associate fellow in the Infectious Diseases Department in Southern Research’s Drug Discovery division. He is interested in finding new potential drugs for influenza and other emerging viruses, particularly those that currently lack approved therapeutics.

His research focuses on three broad areas of viral pathogenesis: (1) viral entry and replication, (2) innate immunity, and (3) drug development. The central premise of this broad approach is to understand basic biology of the emerging pathogens and then use the knowledge to develop inhibitors for the infection.

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Lab Members

Fahim Ahmad, Ph.D.

Fahim Ahmad, Ph.D.

Post-Doctoral Researcher

Dr. Fahim Ahmad obtained his B.S. with honors and an M.S. degree in Biotechnology. Dr. Ahmad next completed his Ph.D. in Molecular Genetics from University of Bundelkhand, Jhansi, India. He completed his first postdoctoral training in the Department of Microbiology and Immunology at the Indiana University School of Medicine in Indianapolis, where his research efforts as a virologist focused on understanding how interaction of HIV-1 (AIDS virus) envelope glycoproteins with host cell receptors leads to membrane fusion and viral entry. He completed his second postdoctoral training at Texas Tech University in El Paso, Texas, where his research focused on the mechanisms of genetic resistance to HIV-1 infection. Later, he joined the University of Texas in El Paso as a Research Scientist and Lecturer where he taught Cellular Immunology at the graduate level and carried out research on T cell-mediated immune control of persistent HIV infection for the purpose of vaccine design. Dr. Ahmad joined Southern Research in 2014. His overall goal is to identify new therapies that target influenza viral replication. A primary concern with the current drugs (amantadines and neuraminidase inhibitors) used to treat influenza is the development of resistant mutations that negate therapeutic benefit. The hypothesis underlying his current research efforts is that compounds that specifically target the polymerase complex might reduce the frequency of escape mutations or promote escape mutants that are unfit for replication. Dr. Ahmad is a member of the Board of Directors for the Integrated Biotechnological Research Institute, is a member of several editorials boards, and serves as a peer reviewer for scientific journals such as General Medical Virology and Center for Neurological Disorders & Drug Targets. Martinez-Gutierrez also described the unprecedented mechanism of action of a unique oleate diol synthase activity in Pseudomonas aeruginosa in prokaryotic cells. He recently described the biological function of the oxylipins derived from the oleate diol synthase activity, being the first report on the role of oxylipins in bacteria. He is currently interested in deciphering the molecular mechanism by which bacteria regulate oxylipin production and their mechanism of action.
Martinez-Gutierrez came to Southern Research from the lab of Dr. François-Xavier Barre at the National Center for Scientific Research (CNRS), France, where he completed a Postdoctoral Research Fellowship working on the molecular biology of V. cholerae filamentous phage CTXΦ.

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