New biochemical insights into the dynamics of water molecules at the GMP or IMP binding site of human GMPR enzyme: A molecular dynamics study.

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 (W1, W2, W3, W4, W5, W7, W8, W9, W10, W12, W13, W15, W17, W18, and W19) are infrequent with dynamic nature. Entrance or displacement of these infrequent water molecules at GMP/IMP sites may occur due to forward and backward movement of reference residues involving ligands. Four water molecules of hGMPR-I and nine water molecules of hGMPR-II are observed in repetitive transitions from GMP to IMP pathway, which indicates discrimination between two isoforms of hGMPRs. Water molecules in cancerous protein are more dynamic and unstable compared to normal protein. These water molecules execute rare dynamical events at GMP binding site and could assist in detailed understanding of conformational transitions that influence the hGMPR's biological functionality. The present study should be of interest to the experimental community engaged in leukemia research and drug discovery for CML cancer.

Investigation of structural analogs of hydroxychloroquine for SARS-CoV-2 main protease (Mpro): A computational drug discovery study.

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 reveals 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.

Structural and Dynamical Impact of Water Molecules at Substrate- or Product-Binding Sites in Human GMPR Enzyme: A Study by Molecular Dynamics Simulations.

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.