The main protease (Mpro) is the key enzyme of nCOVID-19 and plays a decisive role that makes it an attractive drug target. Multiple analysis of crystal structures reveal the presence of W1, W2, and W3 water locations in the active site pocket of Mpro; W1 and W2 are unstable and are weakly bonded with protein in comparison to W3 of Mpro-native. So, we adopt the water displacement method to occupy W1 or W2 sites by triggering HCQ or its analogs to inactivate the enzyme. Virtual screening is employed to find out best analogs of HCQ, molecular docking is used for water displacement from catalytic region of Mpro, and finally, MD simulations are conducted for validation of these findings. The docking study reveals that W1 and W2 are occupied by respective atoms of ZINC28706440 whereas W2 by HCQ and indacaterol. Finally, MD results demonstrate (i) HCQ occupies W1 and W2 positions but its analogs (indacaterol and ZINC28706440) are inadequate to retain either W1 or W2 (ii) His41 and Asp187 are stabilized by W3 in Mpro-native and His41, Cys145 and HCQ by W7 in ZINC28706440, and W4, W5, and W6 make water mediated bridge between indacaterol with His41. The structural, dynamical, and thermodynamic (WFP and J value) profiling parameters suggest that W3, W4, and W7 are prominent in their corresponding positions in comparison with W5 and W6. The final results conclude that ZINC28706440 may act as a best analog of HCQ with acceptable physico-chemical and toxicological scores and may further be synthesized for experimental validation.

Main protease (Mpro) is one of the key enzymes in the life cycle of SARS-CoV-2 that plays a pivotal role in mediating viral replication, transcription, and makes it an attractive drug target for this virus.  The catalytic site of this enzyme comprises of a dyad His41 and Cys145 and lacks the third catalytic residue, which is replaced by a stable water molecule (W). The computational structural analysis on crystal data for Mpro protein suggests that W1, W2, His163, and Tyr161 may also play a vital role in the activity of this enzyme and they may act as catalytic partners along with Cys(145)-His(41) catalytic dyad. The thiolate–imidazolium ion-pair between Cys145 (-SH---NE2-) His41 and Cys145 (-SH---NE2-) His163 have been stabilized by W1 (with W2) and Tyr161, respectively. Therefore, unique interactions of W2---W1---ND1-His41-NE2---SH-Cys145 or Cys145-SH---NE2-His163-ND1---OH-Tyr161 in Mpro serve as an excellent drug target for this enzyme and suggest a rethink of the conventional definition of chemical geometry of inhibitor binding site, its shape, and complementarities. Our computational hypothesis suggests two essential clues that may be implemented to design a new inhibitor for Mpro protein. The strategies are: (i) ligand should be occupied either W1 or W2 or both of these position to displace these water molecules from the catalytic region, and (ii) ligand should be made H-bonds with Cys145 (-SH), His41 (NE2/ND1) and His163(NE2) to inhibit Mpro. The results from this computational study could be of interest to the experimental community and also provide a testable hypothesis for experimental validation. Doi: 10.28991/SciMedJ-2020-02-SI-11 Full Text: PDF

Human guanosine monophosphate reductase (hGMPR) enzyme maintains the intracellular balance between adenine and guanine nucleotide pools, and it is an excellent target for the design of isoform-specific antileukemic agents. In the present study, we have investigated solvation properties of substrate GMP or product inosine-5′-monophosphate (IMP)-binding pocket of hGMPR by employing molecular dynamics simulations on conformations A (substrate GMP), B [substrate GMP with cofactor nicotinamide adenine dinucleotide phosphate (NDP)], C (product IMP with cofactor NDP), and D (product IMP). Nineteen water sites are identified precisely; they are responsible for the catalytic activity of this site, control structural and dynamical integrity, and electronic consequences of GMP or IMP in the binding site of hGMPR. The water sites of category-1 (W1, W4, W5, W6, W13, and W15) in normal protein and category-2 (W2, W3, W7, W8, W10, W17, and W18) in cancerous protein are unique and stabilize the guanosine or inosine group of GMP or IMP for participation in the enzymatic reaction, whereas the remaining water centers either stabilize pentose sugar ribose or the phosphate group of GMP or IMP. Furthermore, water sites of category-4 (W11, W14, and W16) appear to be conserved in all conformations during the entire simulation. The GMP-binding site in cancerous protein 2C6Q is significantly expanded, and its dynamics are very different from normal protein 2BLE. Furthermore, unique interactions of GMP­(N1)···W2···Asp129/Asn158, IMP­(N1)···W3···Glu289, and IMP­(O6)···W10···Ser270 might be used in a water mimic drug design for hGMPR-II. In this context, water finding probability, relative interaction energy (J) associated with water site W, entropy, and topologies of these three water sites are thermodynamically acceptable for the water displacement method by the modified ligand. Hence, their positions in the catalytic pocket may also facilitate future drug discovery for chronic myelogenous leukemia by the design of appropriately oriented chemical groups that may displace these water molecules to mimic their structural, electronic, and thermodynamic properties.

Human GMP reductase (hGMPR) enzyme is involved in a cellular metabolic pathway, converting GMP into IMP, and also it is an important target for anti-leukemic agents.Present computational investigations explain dynamical behavior of water molecules during the conformational transition process from GMP to IMP using molecular dynamics simulations. Residues at substrate-binding site of cancerous protein (PDB Id. 2C6Q) are mostly more dynamic in nature than the normal protein (PDB Id. 2BLE).Nineteen conserved water molecules are identified at the GMP/IMP binding site and are classified as (i) conserved stable dynamic and (ii) infrequent dynamic. Water molecules W11, W14, and W16 are classified as conserved stable dynamic due to their immobile character, whereas remaining water molecules (

The hepatitis E virus (HEV) is a long-ignored virus that has spread globally with time. It ranked 6th among the top risk-ranking viruses with high zoonotic spillover potential; thus, considering its viral threats is a pressing priority. The molecular pathophysiology of HEV infection or the underlying cause is limited. Therefore, we incorporated an unbiased, systematic methodology to get insights into the biological heterogeneity associated with the HEV. Our study fetched 93 and 2016 differentially expressed genes (DEGs) from chronic HEV (CHEV) infection in kidney-transplant patients, followed by hub module selection from a weighted gene co-expression network (WGCN). Most of the hub genes identified in this study were associated with interferon (IFN) signaling pathways. Amongst the genes induced by IFNs, the 2′-5′-oligoadenylate synthase 3 (OAS3) protein was upregulated. Protein-protein interaction (PPI) modular, functional enrichment, and feed-forward loop (FFL) analyses led to the identification of two key miRNAs, i.e., miR-222-3p and miR-125b-5p, which showed a strong association with the OAS3 gene and TRAF-type zinc finger domain containing 1 (TRAFD1) transcription factor (TF) based on essential centrality measures. Further experimental studies are required to substantiate the significance of these FFL-associated genes and miRNAs with their respective functions in CHEV. To our knowledge, it is the first time that miR-222-3p has been described as a reference miRNA for use in CHEV sample analyses. In conclusion, our study has enlightened a few budding targets of HEV, which might help us understand the cellular and molecular pathways dysregulated in HEV through various factors. Thus, providing a novel insight into its pathophysiology and progression dynamics.