Chikungunya virus (CHIKV) is a mosquito-borne arboviral disease. CHIKV belongs to Togaviridae family and Alphavirus genus, consisting of enveloped, positive single-stranded RNA viruses. In humans, there is a rapid onset of CHIKV infection and typically cleared in 5-7 days. It occurs via bite of an infected Aedes aegypi/albopictus, replicates in skin and from there it disseminates to liver and joints via blood. A rapid onset of disease with no pro-dermal phase, following an incubation period of 2-4 days.[1–3] CHIKV enters into the target cells via endocytosis. Upon endocytosis, endosomes undergo conformational change in acidic environments in viral envelope and exposes E1 peptide, mediating virus-host cell membrane fusion. This allows release of viral genome. The viral mRNA translates precursor non-structural proteins (nsps) and undergo cleavage to generate nsp1-nsp4. These nsps such as nsp1 (negative strand viral RNA synthesis), nsp2 (RNA helicase), nsp3 (replicase unit), and nsp4 (viral RNA polymerase).[4–7] Nsps form the replication complex and form RNA intermediates to synthesize sub-genomic (26S) and genomic (49S) RNAs. Following this, the capsid and glycoproteins are generated, leading to viral assembly by recruiting membrane-associated glycoproteins. It consists of capsid (C) protein that forms nucleocapsid. The envelope of viral particle consists of E1 and E2 transmembrane glycoproteins that arrange into 80 spikes with three E1/2 heterodimer. The E1 and E2 facilitates membrane fusion and binding to the host cell, respectively. Its genome consists of two ORFs that are flanked by 5’ and 3’ UTRs and separated by non-coding intergenic region. The ORF1 and ORF2 encodes for nsp1-4 and structural proteins such as capsid, glycoprotein, virion channel, etc., respectively.[4, 8–11] CHIKV protease (nsp2), has a catalytic dyad (Cys1013/His1083) that processes viral polyproteins. Further, it has also been suggested that the catalytic dyad is interchangeable to a serine (proximal) and hence making called non-papain-like cysteine protease. Similarly, nsp3 plays important role during replication of CHIKV genome.[2, 12, 13]
Molecular dynamics (MD) simulations is a time-saving, computational approach to perform molecular docking and provides the energy for complex formation between the receptor and a small molecule. Temperature-dependent MD simulation can be performed to understand the impact of temperature on the activity of non-structural protease of CHIKV. Upon screening of a small molecule against the nsp of CHIKV, at fluctuating temperatures, gives the binding energy for the complex formation that may vary with temperature. The temperature-dependent MD simulations would give different trajectories that can be analyzed to understand the change in the nsp.[9, 11, 14–17] MD simulation is a computer simulation-based approach that analyze physical movements of atoms, molecules and biomacromolecules such as protein, DNA and more. It’s an important and effective approach to study physical and chemical changes of small molecules. MD simulations combining with Newton’s second law of motion to obtain an output of MD simulation trajectories, which are snapshots of simulated molecular system, representing atomic coordinates at specific time periods. The trajectories are generated by Newton’s second law of motion for time evaluation of n interacting particles.[9, 14, 18–20]
We all witness to various viral infection; have threatened the humanity. Researchers are working on the inhibition of the virus through experimental work as well as computational methodologies to get the effective or promising inhibitors. Authors have considered non-structural protease-2 (nsp2) and non-structural protease-3 (nsp3) of CHIKV for the investigation as they are involved in the replication of the virus and increases the infections in the human. In this work, the impact of temperature on non-structural protease-2 and non-structural protease-3 of CHIKV has been investigated using the molecular dynamics simulations for 100 ns at 300, 325 and 350 K.