Structural and Computational Studies of Cobalt(II) and Copper(II) Complexes with Aromatic Heterocyclic Ligand

Two coordination complexes, a cobalt(II) complex tris(1,10-phenanthroline)-cobalt perchlorate hydrate, [Co(phen)3]·(ClO4)2·H2O(1), and a copper(II) complex tris(1,10-phenanthroline)-copper perchlorate 4-bromo-2-{[(naphthalene-1-yl)imino]methyl}phenol hydrate, [Cu(phen)3]·(ClO4)2·HL·[O] (2), [where, phen = 1,10-phenathroline as aromatic heterocyclic ligand, HL = 4-bromo-2-((Z)-(naphthalene-4-ylimino) methyl) phenol] have been synthesized and structurally characterized. Single crystal X-ray analysis of both complexes has revealed the presence of a distorted octahedral geometry around cobalt(II) and copper(II) ions. density functional theory (DFT)-based quantum chemical calculations were performed on the cationic complex [Co(phen)3]2+ and copper(II) complex [Cu(phen)3]2+ to get the structure property relationship. Hirshfeld surface and 2-D fingerprint plots have been explored in the crystal structure of both the metal complexes. To find potential SARS-CoV-2 drug candidates, both the complexes were subjected to molecular docking calculations with SARS-CoV-2 virus (PDB ID: 7BQY and 7C2Q). We have found stable docked structures where docked metal chelates could readily bound to the SARS-CoV-2 Mpro. The molecular docking calculations of the complex (1) into the 7C2Q-main protease of SARS-CoV-2 virus revealed the binding energy of −9.4 kcal/mol with a good inhibition constant of 1.834 µM, while complex (2) exhibited the binding energy of −9.0 kcal/mol, and the inhibition constant of 1.365 µM at the inhibition binding site of receptor protein. Overall, our in silico studies explored the potential role of cobalt(II) complex (1), and copper(II) complex (2) complex as the viable and alternative therapeutic solution for SARS-CoV-2.

Comparative Study of Molecular Docking, Structural, Electronic, and Fukui Function Studies on Favipiravir and its Newly Designed Derivatives (Potential Inhibitors) for COVID-19 Protease

Favipiravir is an antiviral medication currently being trialed as a COVID-19 treatment. These results motivate us to develop new species (possibly drugs) from favipiravir, perform comparative molecular docking, and reexamine their biological and pharmacological activities. Detailed quantum chemical research on favipiravir and its newly designed derivatives has been carried out with the help of DFT/B3LYP/6–311 + + G (d, p). In the present work, the structure of favipiravir has been modified and 12 new species have been modeled (all species are inherently stable because no virtual frequency is found during the vibration analysis). Reactivity of all species using various descriptors (local) such as Fukui function, local softness, electrophilicity, and global, i.e., electronegativity, hardness, HOMO–LUMO gap, etc. of the same are calculated and discussed. In silico studies such as molecular docking of all species and complete quantum chemistry studies suggest that four of them may mitigate the effects of the COVID-19 protease. © 2023 Wiley-VCH GmbH.

Electronic, intermolecular, quantum computational investigations, molecular docking and simulation studies of the potent antiviral drug EIDD-2801

In this work, an analysis has been done to describe the molecular structure, spectroscopic, reduced density gradient, topological properties, atomic charges, Lipinski rule, Natural bond orbital analysis, docking and molecular dynamics simulation of the potent antiviral drug EIDD-2801 in the effective treatment against COVID-19. Intramolecular charge distribution is well understood by three schemes such as AIM, Mulliken and NBO analysis and non-covalent interactions have been understood through reduced density gradient. Topological properties, such as charge density and Laplacian of charge density along with the electron localization function, make it easy to obtain comprehensive information about bond strengths and critical points. The details obtained from the calculation of global reactivity descriptors and Lipinski rule are useful for understanding the nature of molecular reactivity and site selectivity. Electrostatic potentials help to identify potential electrophilic and nucleophilic sites for interaction between EIDD-2801 and target proteins. The molecular docking combined with molecular dynamic simulation studies enables us to get better picture about the ligand-protein interaction.Copyright © 2023 Indian Chemical Society

Coherent Phonons in Antimony: An Undergraduate Physical Chemistry Solid-State Ultrafast Laser Spectroscopy Experiment

Ultrafast laser pump-probe spectroscopy is an important and growing field of physical chemistry that allows the measurement of chemical dynamics on their natural time scales, but undergraduate laboratory courses lack examples of such spectroscopy and the interpretation of the dynamics that occur. Here we develop and implement an ultrafast pump-probe spectroscopy experiment for the undergraduate physical chemistry laboratory course at the University of California Berkeley. The goal of the experiment is to expose students to concepts in solid-state chemistry and ultrafast spectroscopy via classic coherent phonon dynamics principles developed by researchers over multiple decades. The experiment utilizes a modern high-repetition-rate 800 nm femtosecond Ti:sapphire laser, split pulses with a variable time delay, and sensitive detection of transient reflectivity signals using the lock-in technique. The experiment involves minimal intervention from students and is therefore easy and safe to implement in the laboratory. Students first perform an intensity autocorrelation measurement on the femtosecond laser pulses to obtain their temporal duration. Then, students measure the pump-probe reflectivity of a single-crystal antimony sample to determine the period of coherent phonon oscillations initiated by an ultrafast pulse excitation, which is analyzed by fitting to a sine wave. Students who completed the experiment in-person obtained good experimental results, and students who took the course remotely due to the COVID-19 pandemic were provided with the data they would have obtained during the experiment to analyze. Evaluation of student written and oral reports reveals that the learning goals were met, and that students gained an appreciation for the field of ultrafast laser-induced chemistry. © 2022 American Chemical Society and Division of Chemical Education, Inc.

Virtual Screening and Quantum Chemistry Analysis for SARS-CoV-2 RNA-Dependent RNA Polymerase Using the ChEMBL Database: Reproduction of the Remdesivir-RTP and Favipiravir-RTP Binding Modes Obtained from Cryo-EM Experiments with High Binding Affinity.

The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the pathogenic cause of coronavirus disease 2019 (COVID-19). The RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 is a potential target for the treatment of COVID-19. An RdRp complex:dsRNA structure suitable for docking simulations was prepared using a cryo-electron microscopy (cryo-EM) structure (PDB ID: 7AAP; resolution, 2.60 Å) that was reported recently. Structural refinement was performed using energy calculations. Structure-based virtual screening was performed using the ChEMBL database. Through 1,838,257 screenings, 249 drugs (37 approved, 93 clinical, and 119 preclinical drugs) were predicted to exhibit a high binding affinity for the RdRp complex:dsRNA. Nine nucleoside triphosphate analogs with anti-viral activity were included among these hit drugs, and among them, remdesivir-ribonucleoside triphosphate and favipiravir-ribonucleoside triphosphate adopted a similar docking mode as that observed in the cryo-EM structure. Additional docking simulations for the predicted compounds with high binding affinity for the RdRp complex:dsRNA suggested that 184 bioactive compounds could be anti-SARS-CoV-2 drug candidates. The hit bioactive compounds mainly consisted of a typical noncovalent major groove binder for dsRNA. Three-layer ONIOM (MP2/6-31G:AM1:AMBER) geometry optimization calculations and frequency analyses (MP2/6-31G:AMBER) were performed to estimate the binding free energy of a representative bioactive compound obtained from the docking simulation, and the fragment molecular orbital calculation at the MP2/6-31G level of theory was subsequently performed for analyzing the detailed interactions. The procedure used in this study represents a possible strategy for discovering anti-SARS-CoV-2 drugs from drug libraries that could significantly shorten the clinical development period for drug repositioning.

New Chemicals Suppressing SARS-CoV-2 Replication in Cell Culture.

Candidates to being inhibitors of the main protease (Mpro) of SARS-CoV-2 were selected from the database of Voronezh State University using molecular modeling. The database contained approximately 19,000 compounds represented by more than 41,000 ligand conformers. These ligands were docked into Mpro using the SOL docking program. For one thousand ligands with best values of the SOL score, the protein-ligand binding enthalpy was calculated by the PM7 quantum-chemical method with the COSMO solvent model. Using the SOL score and the calculated protein-ligand binding enthalpies, eighteen compounds were selected for the experiments. Several of these inhibitors suppressed the replication of the coronavirus in cell culture, and we used the best three among them in the search for chemical analogs. Selection among analogs using the same procedure followed by experiments led to identification of seven inhibitors of the SARS-CoV-2 replication in cell culture with EC50 values at the micromolar level. The identified inhibitors belong to three chemical classes. The three inhibitors, 4,4-dimethyldithioquinoline derivatives, inhibit SARS-CoV-2 replication in Vero E6 cell culture just as effectively as the best published non-covalent inhibitors, and show low cytotoxicity. These results open up a possibility to develop antiviral drugs against the SARS-CoV-2 coronavirus.

Quantum Chemical Studies on SARS-CoV-2-a Review

As soon as foreign substances like bacteria, fungi, chemicals and viruses (antigens) enter a human body, a protective protein (mostly Y-shaped), known as an antibody (immunoglobulin G - IgG) is produced by our immune system. But antibodies are not that much effective against viruses. Because viruses tend to mutate that leads to change in their shape which disturbs the necessitation of shape complementarity which limits the effectiveness of the antibody. Coronaviridae is a family of viruses that are responsible for SARS-CoV-2 (COVID-19) infection which is a contagious and serious viral infection. These spreads breathing of viral drops coming out of coughing and sneezing of infected persons. Touching of infected surface is also a prime cause of infection. Vaccines tend to train and prepare our body's immune system to recognize and fight off the infectious foreign bodies when they enter. After vaccination, if the antigens enter our body later, our immune system will be immediately ready to destroy them to prevent sickness. Lot of factors like vaccine inefficiency to different variants of existing viruses, age factor, denial of vaccination and previously existing illness make the issue still critical. To face this deadly, alarming global challenge and to prevent the future coronavirus outbreaks, various scientific communities have been toiling in multiple diverse studies about this newly emerged virus. In this review, we underline and summarize the recent research findings involving the SARS-CoV-2's structure, character, lifecycle, its target, finding out antivirus drugs (mainly S-protein of SARS-CoV-2 is targeted), inhibitors, a protocol to identify anti-COVID-19 candidates, detection of efficient and approved vaccines etc. © 2022 IEEE.

Novel Inhibitors of 2'-O-Methyltransferase of the SARS-CoV-2 Coronavirus.

The COVID-19 pandemic is still affecting many people worldwide and causing a heavy burden to global health. To eliminate the disease, SARS-CoV-2, the virus responsible for the pandemic, can be targeted in several ways. One of them is to inhibit the 2'-O-methyltransferase (nsp16) enzyme that is crucial for effective translation of viral RNA and virus replication. For methylation of substrates, nsp16 utilizes S-adenosyl methionine (SAM). Binding of a small molecule in the protein site where SAM binds can disrupt the synthesis of viral proteins and, as a result, the replication of the virus. Here, we performed high-throughput docking into the SAM-binding site of nsp16 for almost 40 thousand structures, prepared for compounds from three libraries: Enamine Coronavirus Library, Enamine Nucleoside Mimetics Library, and Chemdiv Nucleoside Analogue Library. For the top scoring ligands, semi-empirical quantum-chemical calculations were performed, to better estimate protein-ligand binding enthalpy. Relying upon the calculated binding energies and predicted docking poses, we selected 21 compounds for experimental testing.

Exploring the inhibitory potential of novel bioactive compounds from mangrove actinomycetes against nsp10 the major activator of SARS-CoV-2 replication.

The current study reveals the inhibitory potential of novel bioactive compounds of mangrove actinomycetes against nsp10 of SARS-CoV-2. A total of fifty (50) novel bioactive (antibacterial, antitumor, antiviral, antioxidant, and anti-inflammatory) compounds of mangrove actinomycetes from different chemical classes such as alkaloids, dilactones, sesquiterpenes, macrolides, and benzene derivatives are used for interaction analysis against nsp10 of SARS-CoV-2. The six antiviral agents sespenine, xiamycin c, xiamycin d, xiamycin e, xiamycin methyl ester, and xiamycin A (obeyed RO5 rule) are selected based on higher binding energy, low inhibition constant values, and better-docked positions. The effective hydrogen and hydrophobic (alkyl, π -sigma, π - π T shaped and π -alkyl) interaction analysis reveals the four antivirals sespenine, xiamycin C, xiamycin methyl ester, and xiamycin A are supposed to be the most auspicious inhibitors against nsp10 of SARS-CoV-2. Quantum chemistry methods such as frontier molecular orbitals and molecular electrostatic potential are used to explain the thermal stability and chemical reactivity of ligands. The toxicity profile shows that selected ligands are safe by absorption, distribution, metabolism, excretion, and toxicity profiling and also effective for inhibition of nsp10 protein of SARS-CoV-2. The molecular dynamic simulation investigation of apo and halo forms of nsp10 done by RMSD of C α atoms of nsp10, all amino acid residues RMSF, count total number of hydrogen bonds and radius of gyration (R g). MD simulations reveal the complexes are stable and increase the structural compactness of nsp10 in the binding pocket. The lead antiviral compounds sespenine, xiamycin C, xiamycin methyl ester, and xiamycin A are recommended as the most promising inhibitors against nsp10 of SARS-CoV-2 pathogenicity. Supplementary Information: The online version contains supplementary material available at 10.1007/s11696-021-01997-x.

Thermally Activated Charge Transfer in Dual-Emission Mn2+-Alloyed Perovskite Quantum Wells for Luminescent Thermometers

Owing to the pandemic of Coronavirus disease 2019 (COVID-19), the demands on ultracold-chain logistics have rapidly increased for the storage and transport of mRNA vaccines. Herein, we report a soluble luminescent thermometer based on thermally activated dual-emissions of Mn2+-alloyed 2D perovskite quantum wells (QWs). Owing to the Mn2+ alloying, the binding energy of perovskite QW exciton is reduced from 291 to 100 meV. It facilitates the dissociation of excitons into free charge carriers, which are then transferred and trapped on Mn2+. The temperature-dependent charge transfer efficiency can be tuned from 8.8% (-93 °C) to 30.6% (25 °C), leading to continuous ratiometrical modulation from exciton-dominated violet emission to Mn2+-dominated orange emission. The highest sensitivity (1.44% per K) is approximately twice that of the Mn2+-doped chalcogenide quantum dots. Taking advantage of highly reversible color switching, Mn2+-alloyed QWs provide an economical solution to monitor the ultracold-chain logistics of the COVID-19 vaccine. © 2022 American Chemical Society.

Application of Docking and Quantum Chemistry to the Search for Inhibitors of SARS-CoV-2 Main Protease

Docking and quantum-chemical molecular modeling methods have been applied to search inhibitors of the main protease of SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic. More than 14 thousand organic compounds from the commercially available Maybridge database were docked into the active site of main protease using the SOL docking program, and more than 100 ligands with the most negative SOL scores were selected for further processing. For all these top scored ligands, the enthalpy of protein-ligand binding was calculated using the PM7 semiempirical quantum-chemical method with the COSMO implicit solvent model. When calculating the enthalpy of protein-ligand binding, a best docked ligand pose was used as the initial conformation for local energy optimization by the PM7 method with varying the positions of all ligand atoms. In the optimized ligand pose, the energy of the protein-ligand complex was recalculated with the COSMO solvent for fixed positions of all atoms of the system. For further experimental testing, 18 ligands were selected with the following criteria: good SOL scores, the most negative binding enthalpies, favorable protein-ligand interactions inferred from visual inspection of the docking poses and chemical diversity of the ligands. The selected ligands are planned to be measured in vitro for their inhibition of the main protease SARS-CoV-2. In the case of experimental confirmation of their inhibitory activity, these compounds can be used to further optimize their chemical structure in order to obtain a lead compound – the basis for new direct-acting antiviral drugs against the SARS-CoV-2 coronavirus. © 2021, Springer Nature Switzerland AG.

Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations.

The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the energy of the protein-ligand complex calculated by the quantum-chemical method. In quantum quasi-docking, firstly, we look for a wide spectrum of low-energy minima, calculated using the MMFF94 force field, and secondly, we recalculate the energies of all these minima using the quantum-chemical method, and among these recalculated energies we determine the lowest energy and the corresponding ligand position. Both PM6-D3H4X and PM7 are novel methods that describe well-dispersion interactions, hydrogen and halogen bonds. The PM6-D3H4X and PM7 methods are used with the COSMO implicit solvent model as it is implemented in the MOPAC program. The comparison is made for 25 high quality protein-ligand complexes. Firstly, the docking positioning accuracies have been compared, and we demonstrated that PM7+COSMO provides better positioning accuracy than PM6-D3H4X. Secondly, we found that PM7+COSMO demonstrates a much higher correlation between the calculated and measured protein-ligand binding enthalpies than PM6-D3H4X. For future quantum docking PM7+COSMO is preferable, but the COSMO model must be improved.

[Development of antiviral drugs based on inhibitors of the SARS-COV-2 main protease]. / Razrabotka protivovirusnykh lekarstv na osnove ingibitorov glavnoi proteazy SARS-CoV-2.

Docking and quantum-chemical methods have been used for screening of drug-like compounds from the own database of the Voronezh State University to find inhibitors the SARS-CoV-2 main protease, an important enzyme of the coronavirus responsible for the COVID-19 pandemic. Using the SOL program more than 42000 3D molecular structures were docked into the active site of the main protease, and more than 1000 ligands with most negative values of the SOL score were selected for further processing. For all these top ligands, the protein-ligand binding enthalpy has been calculated using the PM7 semiempirical quantum-chemical method with the COSMO implicit solvent model. 20 ligands with the most negative SOL scores and the most negative binding enthalpies have been selected for further experimental testing. The latter has been made by measurements of the inhibitory activity against the main protease and suppression of SARS-CoV-2 replication in a cell culture. The inhibitory activity \of the compounds was determined using a synthetic fluorescently labeled peptide substrate including the proteolysis site of the main protease. The antiviral activity was tested against SARS-CoV-2 virus in the Vero cell culture. Eight compounds showed inhibitory activity against the main protease of SARS-CoV-2 in the submicromolar and micromolar ranges of the IC50 values. Three compounds suppressed coronavirus replication in the cell culture at the micromolar range of EC50 values and had low cytotoxicity. The found chemically diverse inhibitors can be used for optimization in order to obtain a leader compound, the basis of new direct-acting antiviral drugs against the SARS-CoV-2 coronavirus.