The spectroscopic (FTIR, FT-Raman, NMR and UV), first-order hyperpolarizability and HOMO-LUMO analysis of methylboronic acid

Computational discovery of dual potential inhibitors of SARS-CoV-2 spike/ACE2 and Mpro: 3D-pharmacophore, docking-based virtual screening, quantum mechanics and molecular dynamics

To find drugs against COVID-19, caused by the SARS-CoV-2, promising targets include the fusion of the viral spike with the human angiotensin-converting enzyme 2 (ACE2) as well as the main protease (Mpro). These proteins are responsible for viral entry and replication, respectively. We combined several state-of-the-art computational methods, including, protein-ligand interaction fingerprint, 3D-pharmacophores, molecular-docking, MM-GBSA, DFT, and MD simulations to explore two databases: ChEMBL and NANPDB to identify molecules that could both block spike/ACE2 fusion and inhibit Mpro. A total of 1,690,649 compounds from the two databases were screened using the pharmacophore model obtained from PLIF analysis. Five recent complexes of Mpro co-crystallized with different ligands were used to generate the pharmacophore model, allowing 4,829 compounds that passed this prefilter. These were then submitted to molecular docking against Mpro. The 5% top-ranked docking hits from docking result having scores < -8.32 kcal mol-1 were selected and then docked against spike/ACE2. Only four compounds: ChEMBL244958, ChEMBL266531, ChEMBL3680003, and 1-methoxy-3-indolymethyl glucosinolate (4) displayed binding energies < - 8.21 kcal mol-1 (for the native ligand) were considered as putative dual-target inhibitors. Furthermore, predictive ADMET, MM-GBSA and DFT/6-311G(d,p) were performed on these compounds and compared with those of well-known antivirals. DFT calculations showed that ChEMBL244958 and compound 4 had significant predicted reactivity values. Molecular dynamics simulations of the docked complexes were run for 100 ns and used to validate the stability docked poses and to confirm that these hits are putative dual binders of the spike/ACE2 and the Mpro.

Identification of potential phytochemicals from Citrus Limon against main protease of SARS-CoV-2: molecular docking, molecular dynamic simulations and quantum computations

The outbreak of coronavirus disease (COVID-19) caused by a novel RNA virus emerged at the end of 2019. Most of the patient's symptoms are mild to moderate, and influenza, acute respiratory distress syndrome (ARDS) and multi-organ failure are common. The disease is mild to moderate in most patients and is reported in many cases such as pneumonia, ARDS and multi-organ dysfunction. This study's objective is to evaluate 25 natural compounds from Citrus limon (CL) used by comprehensive molecular docking, density functional theory (DFT) and molecular dynamics analysis against SARS-CoV-2 main protease (M^pro). Among all the experimental compounds, diosmetin has shown the best docking values against the M^pro of SARS-CoV-2 compared to the standard antiviral drug. In DFT calculations, the order associated with biochemical reactivity is as follows: eriodictoyl > quercetin > spinacetin > diosmetin > luteolin > apigenin, whereas the regions of oxygen and hydrogen atoms from the selected isolated compounds are appropriate for electrophilic and nucleophilic attacks, respectively. Also, HOMO-LUMO and global descriptors values indicated a promising result of these compounds. Moreover, a molecular dynamics simulation study revealed the stable conformation and binding pattern in a stimulating environment of natural compounds CL. Considering molecular docking, simulation, and DFT analysis of the selected compounds, notably eriodictoyl, quercetin, and diosmetin showed good potential against SARS-CoV-2 M^pro. Our in silico study revealed promising antiviral activity, which may be considered a potential key factor or a therapeutic target for COVID-19.Communicated by Ramaswamy H. Sarma.

Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study

Since the outbreak of the COVID-19 (coronavirus disease 19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The present study aimed to evaluate bioactive compounds found in plants using a molecular docking approach to inhibit the main protease (Mpro) and spike (S) glycoprotein of SARS-CoV-2. The evaluation was performed on the docking scores calculated using AutoDock Vina (AV) as a docking engine. A rule of five (Ro5) was calculated to determine whether a compound meets the criteria as an active drug orally in humans. The determination of the docking score was performed by selecting the best conformation of the protein-ligand complex that had the highest affinity (most negative Gibbs' free energy of binding/ΔG). As a comparison, nelfinavir (an antiretroviral drug), chloroquine, and hydroxychloroquine sulfate (antimalarial drugs recommended by the FDA as emergency drugs) were used. The results showed that hesperidin, nabiximols, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine, and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and nabiximols had about the same pose as nelfinavir but were better than chloroquine and hydroxychloroquine sulfate as Mpro inhibitors. This finding implied that several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine, and hydroxychloroquine sulfate, which so far are recommended in the treatment of COVID-19. From quantum chemical DFT calculations, the ascending order of chemical reactivity of selected compounds was pectolinarin > hesperidin > rhoifolin > morin > epigallocatechin gallate. All isolated compounds' C=O regions are preferable for an electrophilic attack, and O-H regions are suitable for a nucleophilic attack. Furthermore, Homo-Lumo and global descriptor values indicated a satisfactory remarkable profile for the selected compounds. As judged by the RO5 and previous study by others, the compounds kaempferol, herbacetin, eugenol, and 6-shogaol have good oral bioavailability, so they are also seen as promising candidates for the development of drugs to treat infections caused by SARS-CoV-2. The present study identified plant-based compounds that can be further investigated in vitro and in vivo as lead compounds against SARS-CoV-2.

Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study

Since the outbreak of the COVID-19 (coronavirus disease 19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The present study aimed to evaluate bioactive compounds found in plants using a molecular docking approach to inhibit the main protease (M^pro) and spike (S) glycoprotein of SARS-CoV-2. The evaluation was performed on the docking scores calculated using AutoDock Vina (AV) as a docking engine. A rule of five (Ro5) was calculated to determine whether a compound meets the criteria as an active drug orally in humans. The determination of the docking score was performed by selecting the best conformation of the protein-ligand complex that had the highest affinity (most negative Gibbs' free energy of binding/ΔG). As a comparison, nelfinavir (an antiretroviral drug), chloroquine, and hydroxychloroquine sulfate (antimalarial drugs recommended by the FDA as emergency drugs) were used. The results showed that hesperidin, nabiximols, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine, and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and nabiximols had about the same pose as nelfinavir but were better than chloroquine and hydroxychloroquine sulfate as M^pro inhibitors. This finding implied that several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine, and hydroxychloroquine sulfate, which so far are recommended in the treatment of COVID-19. From quantum chemical DFT calculations, the ascending order of chemical reactivity of selected compounds was pectolinarin > hesperidin > rhoifolin > morin > epigallocatechin gallate. All isolated compounds' C=O regions are preferable for an electrophilic attack, and O-H regions are suitable for a nucleophilic attack. Furthermore, Homo-Lumo and global descriptor values indicated a satisfactory remarkable profile for the selected compounds. As judged by the RO5 and previous study by others, the compounds kaempferol, herbacetin, eugenol, and 6-shogaol have good oral bioavailability, so they are also seen as promising candidates for the development of drugs to treat infections caused by SARS-CoV-2. The present study identified plant-based compounds that can be further investigated in vitro and in vivo as lead compounds against SARS-CoV-2.

FT-IR, FT-Raman, NMR and UV-Vis spectra and DFT calculations of 5-bromo-2-ethoxyphenylboronic acid (monomer and dimer structures)

In this study, the Fourier Transform Infrared (FT-IR) and Fourier Transform Raman (FT-Raman) spectra of 5-bromo-2-ethoxyphenylboronic acid (5Br2EPBA) are recorded in the solid phase in the region 4000-400 cm(-1) and 3500-10 cm(-1), respectively. The (1)H, (13)C and DEPT nuclear magnetic resonance (NMR) spectra are recorded in DMSO solution. The UV-Vis absorption spectrum of 5Br2EPBA is saved in the range of 200-400 nm in ethanol and water. The following theoretical calculations for monomeric and dimeric structures are supported by experimental results. The molecular geometry and vibrational frequencies in the ground state are calculated by using DFT methods with 6-31G(d,p) and 6-311G(d,p) basis sets. There are four conformers for the present molecule. The computational results diagnose the most stable conformer of 5Br2EPBA as Trans-Cis (TC) form. The complete assignments are performed on the basis of the total energy distribution (TED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method in parallel quantum solutions (PQS) program. The (1)H and (13)C NMR chemical shifts of 5Br2EPBA molecule are calculated by using the Gauge Invariant Atomic Orbital (GIAO) method in DMSO and gas phase for monomer and dimer structures of the most stable conformer. Moreover, electronic properties, such as the HOMO and LUMO energies (by TD-DFT and CIS methods) and molecular electrostatic potential surface (MEPs) are investigated. Stability of the molecule arising from hyper-conjugative interactions, charge delocalization is analyzed using natural bond orbital (NBO) analysis. Nonlinear optical (NLO) properties and thermodynamic features are presented. All calculated results are compared with the experimental data of the title molecule. The correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the title molecule.

DFT calculations and experimental FT-IR, FT-Raman, NMR, UV-Vis spectral studies of 3-fluorophenylboronic acid

The spectroscopic (FT-IR, FT-Raman, (1)H and (13)C NMR, UV-Vis), structural, electronic and thermodynamical properties of 3-fluorophenylboronic acid (C6H4FB(OH)2), 3FPBA) were submitted by using both experimental techniques and theoretical methods (quantum chemical calculations) in this work. The experimental infrared and Raman spectra were obtained in the region 4000-400 cm(-1) and 3500-10 cm(-1), respectively. The equilibrium geometry and vibrational spectra were calculated by using DFT (B3LYP) with 6-311++G(d,p) basis set. The vibrational wavenumbers were also corrected with scale factor to take better results for the calculated data. The total energy distributions (TED) of the vibrational modes were performed for the assignments of the title molecule by using scaled quantum mechanics (SQM) method. The NMR chemical shifts ((1)H and (13)C) were recorded in DMSO solution. The (1)H and (13)C NMR spectra were computed by using the gauge-invariant atomic orbital (GIAO) method, showing a good agreement with the experimental ones. The last one UV-Vis absorption spectra were analyzed in two solvents (ethanol and water), saved in the range of 200-400 nm. In addition these, HOMO and LUMO energies, the excitation energies, density of states (DOS) diagrams, thermodynamical properties and molecular electrostatic potential surface (MEPs) were presented. Nonlinear optical (NLO) properties and thermodynamic features were performed. The experimental results are combined with the theoretical calculations using DFT calculations to fortification of the paper. At the end of this work, the results were proved our paper had been indispensable for the literature backing.

Interactions of "bora-penicilloates" with serine β-lactamases and DD-peptidases

Specific boronic acids are generally powerful tetrahedral intermediate/transition state analogue inhibitors of serine amidohydrolases. This group of enzymes includes bacterial β-lactamases and DD-peptidases where there has been considerable development of boronic acid inhibitors. This paper describes the synthesis, determination of the inhibitory activity, and analysis of the results from two α-(2-thiazolidinyl) boronic acids that are closer analogues of particular tetrahedral intermediates involved in β-lactamase and DD-peptidase catalysis than those previously described. One of them, 2-[1-(dihydroxyboranyl)(2-phenylacetamido)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid, is a direct analogue of the deacylation tetrahedral intermediates of these enzymes. These compounds are micromolar inhibitors of class C β-lactamases but, very unexpectedly, not inhibitors of class A β-lactamases. We rationalize the latter result on the basis of a new mechanism of boronic acid inhibition of the class A enzymes. A stable inhibitory complex is not accessible because of the instability of an intermediate on its pathway of formation. The new boronic acids also do not inhibit bacterial DD-peptidases (penicillin-binding proteins). This result strongly supports a central feature of a previously proposed mechanism of action of β-lactam antibiotics, where deacylation of β-lactam-derived acyl-enzymes is not possible because of unfavorable steric interactions.

Quantum mechanical study of the structure and spectroscopic (FTIR, FT-Raman), first-order hyperpolarizability and NBO analysis of 1,2-benzoxazol-3-ylmenthane sulfonamide

Fourier transform infrared (FTIR) and FT-Raman spectra of 1,2-benzoxazol-3-ylmenthane sulfonamide in the solid phase were recorded and analyzed. The molecular geometry, vibrational frequencies, infrared intensities, Raman activities and atomic charges were calculated using HF and density functional theory calculation (B3LYP) with standard 6-31G(d, p) basis set. Complete vibrational assignment and analysis of the fundamental modes of the compound were carried out using the observed FTIR and FT-Raman spectra. The thermodynamic functions of the title compound were also performed. Stability of the molecule arising from hyper-conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The dipole moment (μ), polarizability (α) and the hyperpolarizability (β) values of the molecule has been computed. Potential Energy Distribution (PED) were computed for the assignment of unambiguous vibrational fundamental modes. UV-vis spectrum of the compound was also recorded. The theoretical electronic absorption spectra have been calculated by TD-DFT/B3LYP using 6-31G(d,p) basis set. The HOMO and LUMO energy gap reveals that the chemical activity of the molecule. The molecular orbital contributions were studied by density of energy states (DOSs). Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures were calculated. Finally, simulated FTIR and FT-Raman spectra of 1,2-benzoxazol-3-ylmenthane sulfonamide showed good agreement with the observed spectra.

An experimental and theoretical investigation of Acenaphthene-5-boronic acid: conformational study, NBO and NLO analysis, molecular structure and FT-IR, FT-Raman, NMR and UV spectra

The solid state Fourier transform infrared (FT-IR) and FT-Raman spectra of Acenaphthene-5-boronic acid (AN-5-BA), have been recorded in the range 4000-400cm(-1) and 4000-10cm(-1), respectively. Density functional theory (DFT), with the B3LYP functional was used for the optimization of the ground state geometry and simulation of the infrared and Raman spectra of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes and the normal modes were assigned by a scaled quantum mechanical (SQM) force field approach. Hydrogen-bonded dimer of AN-5-BA, optimized by counterpoise correction, has also been studied by B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-H⋯O hydrogen bonding have been discussed. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge-Including Atomic Orbital (GIAO) method. Natural bond orbital (NBO) analysis has been applied to study stability of the molecule arising from charge delocalization. UV spectrum of the title compound was also recorded and the electronic properties, such as frontier orbitals, and band gap energies were measured by TD-DFT approach. The first order hyperpolarizability 〈β〉, its components and associated properties such as average polarizability and anisotropy of the polarizability (α and Δα) of AN-5-BA was calculated using the finite-field approach.

Molecular structure and vibrational spectra of N4-acetylcytosine

The infrared and FT-Raman spectra of N4-acetylcytosine in the solid phase have been recorded, and the molecular geometrical parameters were optimized using B3LYP and MP2 methods with 6-311++G(d,p) basis set. The theoretical calculations indicate the presence of four stable conformers of N4-acetylcytosine, and the one containing an intramoleuclar six-membered ring is the most stable. The vibrational wavenumbers, infrared intensities, Raman scattering activities and the corresponding assignments of the observed bands based on the most optimized conformer were performed by B3LYP methods using the aug-cc-pvtz basis set. The observed and calculated frequencies are found to be in good agreement.

Molecular structure investigation and spectroscopic studies on 2,3-difluorophenylboronic acid: a combined experimental and theoretical analysis

This work presents the characterization of 2,3-difluorophenylboronic acid (abbreviated as 2,3-DFPBA, C(6)H(3)B(OH)(2)F(2)) by quantum chemical calculations and spectral techniques. The spectroscopic properties were investigated by FT-IR, FT-Raman UV-Vis, (1)H and (13)C nuclear magnetic resonance (NMR) techniques. The FT-IR spectrum (4000-400 cm(-1)) and the FT-Raman spectrum (3500-10 cm(-1)) in the solid phase were recorded for 2,3-DFPBA. The (1)H and (13)C NMR spectra were recorded in DMSO solution. The UV-Vis absorption spectra of the 2,3-DFPBA that dissolved in water and ethanol were recorded in the range of 200-400 nm. There are four possible conformers for this molecule. The computational results diagnose the most stable conformer of the 2,3-DFPBA as the trans-cis form. The structural and spectroscopic data of the molecule were obtained for all four conformers from DFT (B3LYP) with 6-311++G (d,p) basis set calculations. The theoretical wavenumbers were scaled and compared with experimental FT-IR and FT-Raman spectra. The complete assignments were performed on the basis of the experimental results and total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method, interpreted in terms of fundamental modes. We obtained good consistency between experimental and theoretical spectra. (13)C and (1)H NMR chemical shifts of the molecule were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. Finally the calculation results were analyzed to simulate infrared, Raman, NMR and UV spectra of the 2,3-DFPBA which show good agreement with observed spectra.