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Highlights • Designed ACE2 lacks enzymatic activity and bears higher thermostability and affinity towards RBD. • The Thr27Arg mutation was introduced to increase the binding affinity against RBD. • The Arg273Gln and Thr445Gly mutations were introduced to reduce the ACE2 enzymatic activity. • The Asp427Arg mutation was done to decrease the flexibility of the ACE2. • The Pro451Met and Gly448Trp mutations were introduced to increase thermostability., The interaction between the angiotensin-converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of the spike protein from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a pivotal role in virus entry into the host cells. Since recombinant ACE2 protein has been suggested as an anti-SARS-CoV-2 therapeutic agent, this study was conducted to design an ACE2 protein with more desirable properties. In this regard, the amino acids with central roles in enzymatic activity of the ACE2 were substituted. Moreover, saturation mutagenesis at the interaction interface between the ACE2 and RBD was performed to increase their interaction affinity. The best mutations to increase the structural and thermal stability of the ACE2 were also selected based on B factors and mutation effects. The obtained resulted revealed that the Arg273Gln and Thr445Gly mutation have drastically reduced the binding affinity of the angiotensin-II into the active site of ACE2. The Thr27Arg mutation was determined to be the most potent mutation to increase the binding affinity. The Asp427Arg mutation was done to decrease the flexibility of the region with high B factor. The Pro451Met mutation along with the Gly448Trp mutation was predicted to increase the thermodynamic stability and thermostability of the ACE2. The designed therapeutic ACE2 would have no enzymatic activity while it could bear stronger interaction with Spike glycoprotein of the SARS-CoV-2. Moreover, decreased in vivo enzymatic degradation would be anticipated due to increased thermostability. This engineered ACE2 could be exploited as a novel therapeutic agent against COVID-19 after necessary evaluations.

Predefined and pre-weighted objective criteria and essential role of Wilms׳ tumor wild type gene (WT1) for maintaining transformed features of cancer cells confirm the high potency of WT1 as a valuable cancer antigen. The antigen was at the top of the ranking among 75 representative cancer antigens. In the present study, an in silico approach was launched to characterized novel CTL epitopes and design a novel multi-epitope DNA vaccine to elicit a desirable immune response against cancers over expressing WT1. Forty-four novel epitopes were described. A multi-epitope construct was designed based on predicted epitopes which is 310 residues in length. The vaccine candidate designed here displays acceptable population coverage (>65%) in different ethnicities as well as high probability of eliciting WT1 antibodies which both are pertinent goals in the context of appropriate multi-epitope vaccines. Various in silico analyses indicate that final vaccine is a qualified immunotherapy candidate capable of eliciting both CD4+ and CD8+ T cell responses.

Listeria monocytogenes , a facultative intracellular fast-growing Gram-positive food-borne pathogen, can infect immunocompromised individuals leading to meningitis, meningoencephalitis and septicaemias. From the pool of virulence factors of the organism, ActA, a membrane protein, has a critical role in the life cycle of L. monocytogenes . High mortality rate of listeriosis necessitates a sensitive and rapid diagnostic test for precise identification of L. monocytogenes . We used bioinformatic tools to locate a specific conserved region of ActA for designing and developing an antibody–antigen based diagnostic test for the detection of L. monocytogenes . A number of databases were looked for ActA related sequences. Sequences were analyzed with several online software to find an appropriate region for our purpose. ActA protein was found specific to Listeria species with no homologs in other organisms. We finally introduced a highly conserved region within ActA sequence that possess several antibody binding sites specific to L. monocytogenes . This protein sequence can serve as an antigen for designing a relatively cheap, sensitive, and specific diagnostic test for detection of L. monocytogenes.

Acinetobacter baumannii is a problematic nosocomial pathogen. The resistance to a wide range of antimicrobial agents, attributable to its biofilm phenotype, makes the treatment very difficult. Biofilm is a common feature of most pathogens. Biofilm associated proteins (Bap) are cellular surface components directly involved in biofilm formation process. The dearth of a fast precise diagnostic test and versatility of Bap sequences in A. baumannii were intuitions to design this study. In silico analysis is a reliable alternative to laborious experimental work in this connection. Databases were searched for an antigenic conserved region of Bap specific to A. baumannii. The region was selected based on alignments and propensity scales. Tertiary structure for this region was built and predicted B-cell epitopes were mapped on the surface of the built model. Our protein subunit was found to be a potential antigen, possessing several antigenic determinants, eliciting antibody. Hence this subunit could be used as a suitable agent for antibody-antigen based diagnostic test. This specific antigen can minimize laboratory errors in identification of A. baumannii and thus help clinicians to quick and precise diagnosis of the bacteria and initiatives to the treatment of the infection. Antigenicity of the region could also be explored for elicitation of antibody to protect the individuals exposed to A. baumannii.