"The whole of science is nothing more than a refinement of everyday thinking" - Albert Einstein
COVID-19 Pandemic Research
In the advent of COVID-19 pandemic, I collaborated with renowned data scientist Dr. Mohammad Ali Moni of the University of Queensland in Australia. I was the lead investigator on several COVID-19 projects under his supervision. I used RNA-seq and microarray data to uncover the regulatory biomarkers (i.e., miRNA, lncRNA, TFs) and molecular pathways involved in COVID-19 severity and their impact on pre-existing health conditions such as cardiovascular disease, diabetes, hypertension, lung cancer, and so on. I also discovered a pathogenetic relationship between SARS-CoV-2 and other SARS-like viruses. Furthermore, I was involved in several drug and vaccine design projects against SARS-CoV-2 spike protein. For example, one study was to identify antiviral selenium-containing heterocyclic compounds that inhibit the SARS-CoV-2 main protease. Another study focused on the ACE2 targeted identification of natural antiviral drug candidates. It is worth noting that our collaboration produced several high-impact papers.
Collaborative Research
Following my MSc degree, I continued my work as a Research Assistant in the Laboratory of Microbiology, Islamic University, Bangladesh. I also became involved in multiple bioinformatics projects related to drug discovery and peptide-based vaccine design. I discovered seven potential QS inhibitors out of more than 100 thousand compounds using a virtual screening pipeline. To do this, I devised a pharmacophore model to detect potential leads that can bind to the active site of the QS receptor LasR protein. A collaborative project also resulted in potential leads against tumor-causing carbonic anhydrase IX protein. In addition, I designed several peptide vaccine candidates against Mycobacterium ulcerans, Elizabethkingia anopheles, Lassa virus, Hantavirus, etc. The modeled vaccine candidates' molecular dynamics and immune simulation studies showed strong binding interactions towards respective TLRs and HLA alleles with robust immune responses. Despite the lack of experimental validation, these computational studies can provide a potential clue for prophylactic development against these pathogens, which have long been neglected.
Post-graduate Research
The quorum sensing (QS) signaling system regulates bacterial biofilm formation, which is a major pathogenic trait in many chronic infections and antibiotic resistance (AR). During my M.Sc. thesis, under the supervision of Prof. Minnatul Karim, I assessed the biofilm formation and AR profiles of different bacterial strains (n=82) from clinical and commensal sources. Notably, clinical bacteria produced 2-fold more biofilm biomass than commensal bacteria, and their respective AR profiles showed a significant positive correlation. This could be attributed to the selection pressure exerted by the frequent use of antibiotics in clinical settings. The project's aim included, of many, the identification of plant-derived compounds as an alternative to antibiotics. I eventually discovered two polyphenols, i.e., quercetin and myricetin, that inhibited biofilm formation and associated virulence in P. aeruginosa by altering QS signaling. Using bioinformatics methods, I found that both compounds competitively inhibit the QS receptor LasR. The whole genome analysis revealed that P. aeruginosa MZ4A has multiple virulence factors that have either evolved or been acquired to thrive in hospital environments.
Collaborators
Mohammad Minnatul Karim, PhD - Islamic University, Bangladesh.
Mohammad Ali Moni, PhD - Queensland University, Australia.
Pietro Lio', PhD - University of Cambridge, England.
Utpal Kumar Adhikari, MSc - Western Sydney University, Australia.
Sudhangshu Kumar Biswas, PhD - Islamic University, Bangladesh.
Shifath Bin Syed, BSc - Washington State University, USA.
Md. Moinuddin Sheam, BSc - Ghent University, Belgium.
Md. Shakil Ahmed Khan, BSc - Seoul National University, Korea.
Swee- Seong Tang, PhD - University of Malaya, Malaysia.
Faruq Abdulla, MSc - Islamic University, Bangladesh.
Foysal Ahammad, MSc - King Abdulaziz University, Saudi Arabia.
Abdus Samad, BSc - Jashore University of Science & Technology, Bangladesh.