Synthesis, anti-bacterial evaluation, DFT study and molecular docking as a potential 3-chymotrypsin-like protease (3CLpro) of SARS-CoV-2 inhibitors of a novel Schiff bases

A Comprehensive Update of Anti-COVID-19 Activity of Heterocyclic Compounds

The Coronavirus disease 2019 (COVID-19) pandemic is one of the most considerable health problems across the world. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the major causative agent of COVID-19. The severe symptoms of this deadly disease include shortness of breath, fever, cough, loss of smell, and a broad spectrum of other health issues such as diarrhea, pneumonia, bronchitis, septic shock, and multiple organ failure. Currently, there are no medications available for coronavirus patients, except symptom-relieving drugs. Therefore, SARS-CoV-2 requires the development of effective drugs and specific treatments. Heterocycles are important constituents of more than 85% of the physiologically active pharmaceutical drugs on the market now. Several FDA-approved drugs have been reported including molnupiravir, remdesivir, ritonavir, oseltamivir, favipiravir, chloroquine, and hydroxychloroquine for the cure of COVID-19. In this study, we discuss potent anti-SARS-CoV-2 heterocyclic compounds that have been synthesized over the past few years. These compounds included; indole, piperidine, pyrazine, pyrimidine, pyrrole, piperazine, quinazoline, oxazole, quinoline, isoxazole, thiazole, quinoxaline, pyrazole, azafluorene, imidazole, thiadiazole, triazole, coumarin, chromene, and benzodioxole. Both in vitro and in silico studies were performed to determine the potential of these heterocyclic compounds in the fight against various SARS-CoV-2 proteins.

Aminoguanidine-based bioactive proligand as AIEE probe for anticancer and anticovid studies

The emission features of a novel bioactive compound, 1,3-bis(2-hydroxy-3,5-diiodophenyl-methylideneamino)guanidine is found impressive with aggregation induced emission enhancement. The nitrogen and iodine rich multidentate proligand was characterized physicochemically. SCXRD and Hirshfeld surface investigation have revealed the presence of significant triangular iodine bonding apart from hydrogen bonding, weak C-H⋯π and π⋯π intermolecular interactions. These interactions collectively contribute to the solid-state packing arrangement of the molecules within the crystal lattice. The band gap of the compound was estimated experimentally and is supported with theoretical calculations. The solid-state fluorescence quantum yield of Φ = 0.36 emphasizes the utility of the proligand and the AIEE characteristics is attributed to restricted intramolecular motions as indicated by fluorescence lifetime decay studies. Strong interaction of the compound with calf thymus DNA was explored experimentally and found to align with in silico docking results. Notably, in vitro anticancer assessment on MCF-7 breast cancer cells show an IC50 value of 181.05 μg mL-1 and signifying its potent cytotoxic properties. Also, the compound is found to have lesser cytotoxicity against L929 normal cell line with an IC50 value of 356.54 μg mL-1. Computational studies further underscore the exceptional binding affinity with active sites in the SARS-CoV-2 main protease 3CLpro, surpassing established repurposed drugs. Furthermore, the proligand demonstrates excellent putative affinity towards the SARS-CoV-2 spike glycoprotein, accompanied by its distinctive AIEE attributes, drug likeness and DNA binding capability rendering it a valuable tool for prospective research investigations.

Molecular guidelines for promising antimicrobial agents

Antimicrobial resistance presents a pressing challenge to public health, which requires the search for novel antimicrobial agents. Various experimental and theoretical methods are employed to understand drug-target interactions and propose multistep solutions. Nonetheless, efficient screening of drug databases requires rapid and precise numerical analysis to validate antimicrobial efficacy. Diptool addresses this need by predicting free energy barriers and local minima for drug translocation across lipid membranes. In the current study employing Diptool free energy predictions, the thermodynamic commonalities between selected antimicrobial molecules were characterized and investigated. To this end, various clustering methods were used to identify promising groups with antimicrobial activity. Furthermore, the molecular fingerprinting and machine learning approach (ML) revealed common structural elements and physicochemical parameters in these clusters, such as long carbon chains, charged ammonium groups, and low dipole moments. This led to the establishment of guidelines for the selection of effective antimicrobial candidates based on partition coefficients (logP) and molecular mass ranges. These guidelines were implemented within the Reinforcement Learning for Structural Evolution (ReLeaSE) framework, generating new chemicals with desired properties. Interestingly, ReLeaSE produced molecules with structural profiles similar to the antimicrobial agents tested, confirming the importance of the identified features. In conclusion, this study demonstrates the ability of molecular fingerprinting and AI-driven methods to identify promising antimicrobial agents with a broad range of properties. These findings deliver substantial implications for the development of antimicrobial drugs and the ongoing battle against antibiotic-resistant bacteria.

Synthesis, Characterizations, and Quantum Chemical Investigations on Imidazo[1,2-a]pyrimidine-Schiff Base Derivative: (E)-2-Phenyl-N-(thiophen-2-ylmethylene)imidazo[1,2-a]pyrimidin-3-amine

In this study, (E)-2-phenyl-N-(thiophen-2-ylmethylene)imidazo[1,2-a]pyrimidin-3-amine (3) is synthesized, and detailed spectral characterizations using 1H NMR, 13C NMR, mass, and Fourier transform infrared (FT-IR) spectroscopy were performed. The optimized geometry was computed using the density functional theory method at the B3LYP/6-311++G(d,p) basis set. The theoretical FT-IR and NMR (1H and 13C) analysis are agreed to validate the structural assignment made for (3). Frontier molecular orbitals, molecular electrostatic potential, Mulliken atomic charge, electron localization function, localized orbital locator, natural bond orbital, nonlinear optical, Fukui functions, and quantum theory of atoms in molecules analyses are undertaken and meticulously interpreted, providing profound insights into the molecular nature and behaviors. In addition, ADMET and drug-likeness studies were carried out and investigated. Furthermore, molecular docking and molecular dynamics simulations have been studied, indicating that this is an ideal molecule to develop as a potential vascular endothelial growth factor receptor-2 inhibitor.

The combination of multi-approach studies to explore the potential therapeutic mechanisms of imidazole derivatives as an MCF-7 inhibitor in therapeutic strategies

Breast cancer covers a large area of research because of its prevalence and high frequency all over the world. This study is based on drug discovery against breast cancer from a series of imidazole derivatives. A 3D-QSAR and activity atlas model was developed by exploring the dataset computationally, using the machine learning process of Flare. The dataset of compounds was divided into active and inactive compounds according to their biological and structural similarity with the reference drug. The obtained PLS regression model provided an acceptable r ² = 0.81 and q² = 0.51. Protein-ligand interactions of active molecules were shown by molecular docking against six potential targets, namely, TTK, HER2, GR, NUDT5, MTHFS, and NQO2. Then, toxicity risk parameters were evaluated for hit compounds. Finally, after all these screening processes, compound C10 was recognized as the best-hit compound. This study identified a new inhibitor C10 against cancer and provided evidence-based knowledge to discover more analogs.

Structural and theoretical investigations, Hirshfeld surface analysis and anti-SARS CoV-2 of nickel (II) coordination complex

A nickel(II) Schiff base complex, [Ni(L)(DMF)](1), was synthesized by treating NiCl₂.6H₂O with an ONS-donor Schiff base ligand(H₂L) derived from the condensation 3,5-Dichlorosalicylaldehyde and 4,4-Dimethyl-3-thiosemicarbazide in DMF. The geometry around the center metal ion in [Ni(L)(DMF)](1) was square planar as revealed by the data collection from diffraction studies. DFT calculations were performed on the complex to get a structure-property relationship. Hirshfeld surface analysis was also carried out in the crystal structure of nickel (II) Schiff base complex. Additionally, inspiring from recent developments to find a potential inhibitor for SARS-CoV-2 virus, we have also performed molecular docking study of [Ni(L)(DMF)](1) to see if our novel complex show affinity for main protease (M^pro) of SARS-CoV-2 M^pro (PDB ID: 6LZE). Interestingly, the results are found quite encouraging where the binding affinity and inhibition constant was found to be -6.6 kcal/mol and 2.358 µM, respectively, for the best docked confirmation of complex [Ni(L)(DMF)](1) with M^pro protein. This binding affinity is reasonably well as compared to recently known antiviral drugs. For instance, the binding affinity of complex [Ni(L)(DMF)](1) is found to be better than that of recently docking results of anti-SARS-CoV-2 drugs like chloroquine (-6.293 kcal/mol), hydroxychloroquine (-5.573 kcal/mol) and remdesivir (-6.352 kcal/mol) when targeted to the active-site of SARS-CoV-2 M^pro. Besides this, molecular docking against G25K GTP-nucleotide binding protein (PDB ID: 1A4R) was also studied. We believe that current results can intrigue not only for the biomedical community but also for the materials chemists who are engaged to explore the application coordination complexes. Communicated by Ramaswamy H. Sarma.

Inhibitory Activity of Saussurea costus Extract against Bacteria, Candida, Herpes, and SARS-CoV-2

Medicinal herbs have long been utilized to treat various diseases or to relieve the symptoms of some ailments for extended periods. The present investigation demonstrates the phytochemical profile, molecular docking, anti-Candida activity, and anti-viral activity of the Saussurea costus acetic acid extract. GC-MS analysis of the extract revealed the presence of 69 chemical compounds. The chemical compounds were alkaloids (4%), terpenoids (79%), phenolic compounds (4%), hydrocarbons (7%), and sterols (6%). Molecular docking was used to study the inhibitory activity of 69 identified compounds against SARS-CoV-2. In total, 12 out of 69 compounds were found to have active properties exhibiting SARS-CoV-2 inhibition. The binding scores of these molecules were significantly low, ranging from -7.8 to -5.6 kcal/mol. The interaction of oxatricyclo [20.8.0.0(7,16)] triaconta-1(22),7(16),9,13,23,29-hexaene with the active site is more efficient. Furthermore, the extract exhibited significant antimicrobial activity (in vitro) against Candida albicans, which was the most susceptible microorganism, followed by Bacillus cereus, Salmonella enterica, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa, respectively. On the other hand, its antiviral activity was evaluated against HSV-1 and SARS-CoV-2, and the results showed a significant positive influence against HSV-1 (EC₅₀ = 82.6 g/mL; CC₅₀ = 162.9 g/mL; selectivity index = 1.9). In spite of this, no impact could be observed in terms of inhibiting the entry of SARS-CoV-2 in vitro.

Development of New Azomethine Metal Chelates Derived from Isatin: DFT and Pharmaceutical Studies

Through the condensation of isatin (indoline-2, 3-dione) and aniline in a 1:1 ratio, a Schiff base ligand was synthesized and characterized via (¹H-NMR, mass, IR, UV-Vis) spectra. Elemental analyses, spectroscopy (¹H-NMR, mass, UV-Vis), magnetic susceptibility, molar conductivity, mass spectra, scanning electron microscope (SEM), and thermal analysis have all been used to characterize a series of Cr(III), Mn(II), Fe(III), Co(II), Ni(II), Cu(II), Zn(II), and Cd(II) metal complexes derived from the titled ligand. The metal-to-ligand ratio is 1:1, according to the analytical data. The Schiff base ligand displayed bidentate behavior with NO coordination sites when it bonded to metal ions, as seen by the IR spectra. The magnetic moment measurement and UV-Vis spectral investigation showed the octahedral geometry of the Cr(III), Fe(III), Co(II), Ni(II), and Zn(II) complexes, whereas they suggested the tetrahedral geometry of the Mn(II), Cu(II), and Cd(II) complexes. The thermal analysis study confirmed the presence of both hydrated and coordinated water molecules in all the compounds, except for the Mn(II) complex, and showed that the complexes decomposed in three or five decomposition steps leaving the corresponding metal oxide as a residue. The ligand and its metal complexes' antibacterial efficacy were evaluated. The findings showed that the metal complexes had stronger antibacterial properties than the ligand alone. The ligand and its metal complexes' anticancer properties were also investigated. A DFT investigation is also reported to gather information regarding the electronic features of the ligand and its metal complexes. Finally, drug-likeness and ADME characteristics were also calculated as parameters.

A computational study of potential therapeutics for COVID-19 invoking conceptual density functional theory

The pandemic, COVID-19, has caused social and economic disruption at a larger pace all over the world. Identification of an effective drug for the deadliest disease is still an exigency. One of the most promising approaches to combat the lethal disease is use of repurposed drugs. This study provides insights into some of the potential repurposed drugs viz. camostat mesylate, hydroxychloroquine, nitazoxanide, and oseltamivir in terms of the computational quantum chemical method. Properties of these compounds have been elucidated in terms of Conceptual Density Functional Theory (CDFT)-based descriptors, IR spectra, and thermochemical properties. Computed results specify that hydroxychloroquine is the most reactive drug among them. Thermochemical data reveals that camostat mesylate has the utmost heat capacity, entropy, and thermal energy. Our findings indicate that camostat mesylate and hydroxychloroquine may be investigated further as potential COVID-19 therapeutics. We anticipate that the current study will aid the scientific community to design and develop viable therapeutics against COVID-19.

Phytochemical Discrimination, Biological Activity and Molecular Docking of Water-Soluble Inhibitors from Saussurea costus Herb against Main Protease of SARS-CoV-2

Siddha medicine is one of the oldest medical systems in the world and is believed to have originated more than 10,000 years ago and is prevalent across ancient Tamil land. It is undeniable that inhibitor preferences rise with increasing solubility in water due to the considerations pertaining to the bioavailability and the ease of which unabsorbed residues can be disposed of. In this study, we showed the phytochemical discrimination of Saussurea costus extracted with water at room temperature as a green extraction procedure. A total of 48 compounds were identified using gas chromatography-mass spectrometry (GC-MS). The fatty acids had a high phytochemical abundance at 73.8%, followed by tannins at 8.2%, carbohydrates at 6.9%, terpenoids at 4.3%, carboxylic acids at 2.5%, hydrocarbons at 2.4%, phenolic compounds at 0.2%, and sterols at 1.5%. Of these compounds, 22 were docked on the active side and on the catalytic dyad of His41 and Cys145 of the main protease of SARS-CoV-2 (M^pro). Eight active inhibitors were carbohydrates, five were fatty acids, three were terpenoids, two were carboxylic acids, one was a tannin, one was a phenolic compound, and one was a sterol. The best inhibitors were 4,8,13-Cyclotetradecatriene-1,3-diol, 1,5,9-trimethyl-12-(1-methylethyl), Andrographolide, and delta.4-Androstene-3.beta.,17.beta.-diol, with a binding affinity that ranged from −6.1 kcal/mol to −6.5 kcal/mol. The inhibitory effect of Saussurea costus of SARS-CoV-2 entry into the cell was studied using a pseudovirus with Spike proteins from the D614G variant and the VOC variants Gamma and Delta. Based on the viral cycle of SARS-CoV-2, our results suggest that the Saussurea costus aqueous extract has no virucidal effect and inhibits the virus in the events after cell entry. Furthermore, the biological activity of the aqueous extract was investigated against HSV-1 virus and two bacterial strains, namely Staphylococcus aureus ATCC BAA 1026 and Escherichia coli ATCC 9637. According to this study, an enormous number of water-soluble inhibitors were identified from Saussurea costus against the M^pro, and this is unprecedented as far as we know.

Bis(thio)carbohydrazone Luminogens with AIEE and ACQ Features and Their In Silico Investigations with SARS-CoV-2

Herein, we report two novel multidentate luminogen proligands bis(3,5-diiodosalicylidene) carbohydrazone (H4L1) and bis(3,5-diiodosalicylidene) thiocarbohydrazone (H4L2), which are suitable candidates for biomedical applications. Though the thiocarbohydrazone H4L2 shows aggregation caused quenching (ACQ), the carbohydrazone H4L1 exhibits stronger fluorescence due to aggregation induced emission enhancement (AIEE). Molecular docking studies of H4L1 and H4L2 along with four similar (thio)carbohydrazones with the active sites of SARS-CoV-2 main protease 3CLpro reveals that the thiocarbohydrazones, in general, are showing better propensity compared to their oxygen analogues. Both the thiocarbohydrazones and the carbohydrazones, however, exhibit better binding potential at the active sites than that of some of the repurposed drugs such as chloroquine, hydroxychloroquine, lopinavir, ritonavir, darunavir and remdesivir. Also, the carbohydrazone H4L1 can be a better bioprobe compared to H4L2 as the former is found to have better binding potential with SARS-CoV-2 spike glycoprotein along with AIEE feature.

Phytochemicals As a Potential Inhibitor of COVID-19: An In-Silico Perspective

The current research has centered on the use of pharmacological and binding affinity methods to test the 36 compounds as bioactive constituents’ inhibitors for COVID-19. Six compounds out of 36 phytoconstituents (rutin, quercetin, catechin gallate, rhamnetin, campesterol and stigmasterol) have demonstrated outstanding molecular docking and drug-like properties as HIV inhibitors Lopinavir and Indinavir. Interestingly, the lowest binding energies (LBE) and the inhibition constant (K_i) have showed that these compounds are able to bind to the P-glycoprotein substrate of 3CL^pro and Nsp15. Interestingly, rutin has been found to be an excellent potential inhibitor for COVID-19 proteins because it has the best LBE score and K_i value than those of other compounds, and of its ability to form strong H-bonds with COVID-19 proteins. The compounds that come next to the rutin compound are stigmasterol and campesterol. As a result, these compounds are considered possible novel inhibitors of COVID-19. In order to validate the computational results, more in vitro and in vivo investigations are required to support the findings of this research.

Synthesis, characterization, in vitro, in silico and in vivo investigations and biological assessment of Knoevenagel condensate β-diketone Schiff base transition metal complexes

A novel Schiff base ligand was synthesized by the Knoevenagel condensation of β-diketone (obtained from substituted Curcumin and Cuminaldehyde) and 4-amino antipyrine. Metal complexes were made from this Schiff base by reacting with metal salts such as Cu(II), Ni(II), Ru(III), VO(IV), and Ce(IV). Physicochemical approaches such as UV-Vis, FT-IR, NMR, EPR, and Mass spectroscopy were used to determine the geometry of the complexes. The thermodynamic stability and biological accessibility of the complexes were investigated using density functional theory (DFT) calculations at the B3LYP/6-31G(d) level. A molecular docking analysis was also performed on 1BNA receptor. Both the Schiff base ligand and metal complexes interacted well to this protein receptor. All metal complexes have a significant potential to bind to CT DNA via the intercalation mechanism. All the in vivo and in vitro screening studies showed that the complexes exhibit higher activities than the free Schiff base.Communicated by Ramaswamy H. Sarma.

Synthesis, crystal structure, computational study and anti-virus effect of mixed ligand copper (II) complex with ONS donor Schiff base and 1, 10-phenanthroline

This work deals with the synthesis, crystal structure, computational study and antiviral potential of mixed ligand copper(II) complex [Cu(L)(phen)](1), (where, H₂L = (Z)-N'-((E)-2-hydroxy-3,5-diiodobenzylidene)-N,N-dimethylcarbamohydrazonothioic acid, phen = 1,10-phenanthroline). The Schiff base ligand (H₂L) is coordinated with Cu(II) ion in O, N, S-tridentate mode. The copper complex (1) crystallized in the monoclinic system of the space group P21/c with eight molecules in the unit cell and reveals a square pyramidal geometry. Furthermore, we also perform quantum chemical calculations to get insights into the structure-property relationship and functional properties of ligand (H₂L) and its copper (II) complex [Cu(L)(phen)](1). Complex [Cu(L)(phen)](1) was also virtually designed in-silico evaluation by Swiss-ADME. Additionally, inspiring by recent developments to find a potential inhibitor for the COVID-19 virus, we have also performed molecular docking study of ligand and its copper complex (1) to see if our compounds shows an affinity for the main protease (M^pro) of COVID-19 spike protein (PDB ID: 7C8U). Interestingly, the results are found quite encouraging where the binding affinity and inhibition constant were found to be -7.14 kcal/mol and 5.82 μM for ligand (H₂L) and -6.18 kcal/mol and 0.76 μM for complex [Cu(L)(phen)](1) with M^pro protein. This binding affinity is reasonably well as compared to recently known antiviral drugs. For instance, the binding affinity of ligand and complex was found to be better than docking results of chloroquine (-6.293 kcal/mol), hydroxychloroquine (-5.573 kcal/mol) and remdesivir (-6.352 kcal/mol) with M^pro protein. The present study may offer the technological solutions and potential inhibition to the COVID-19 virus in the ongoing and future challenges of the global community. In the framework of synthesis and characterization of mixed ligand copper (II) complex; the major conclusions can be drawn as follow.

A Multidisciplinary Approach to Coronavirus Disease (COVID-19)

Since December 2019, humanity has faced an important global threat. Many studies have been published on the origin, structure, and mechanism of action of the SARS-CoV-2 virus and the treatment of its disease. The priority of scientists all over the world has been to direct their time to research this subject. In this review, we highlight chemical studies and therapeutic approaches to overcome COVID-19 with seven different sections. These sections are the structure and mechanism of action of SARS-CoV-2, immunotherapy and vaccine, computer-aided drug design, repurposing therapeutics for COVID-19, synthesis of new molecular structures against COVID-19, food safety/security and functional food components, and potential natural products against COVID-19. In this work, we aimed to screen all the newly synthesized compounds, repurposing chemicals covering antiviral, anti-inflammatory, antibacterial, antiparasitic, anticancer, antipsychotic, and antihistamine compounds against COVID-19. We also highlight computer-aided approaches to develop an anti-COVID-19 molecule. We explain that some phytochemicals and dietary supplements have been identified as antiviral bioproducts, which have almost been successfully tested against COVID-19. In addition, we present immunotherapy types, targets, immunotherapy and inflammation/mutations of the virus, immune response, and vaccine issues.

Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies

Experimental evidence for enzymatic mechanisms is often scarce, and in many cases inadvertently biased by the employed methods. Thus, apparently contradictory model mechanisms can result in decade long discussions about the correct interpretation of data and the true theory behind it. However, often such opposing views turn out to be special cases of a more comprehensive and superior concept. Molecular dynamics (MD) and the more advanced molecular mechanical and quantum mechanical approach (QM/MM) provide a relatively consistent framework to treat enzymatic mechanisms, in particular, the activity of proteolytic enzymes. In line with this, computational chemistry based on experimental structures came up with studies on all major protease classes in recent years; examples of aspartic, metallo-, cysteine, serine, and threonine protease mechanisms are well founded on corresponding standards. In addition, experimental evidence from enzyme kinetics, structural research, and various other methods supports the described calculated mechanisms. One step beyond is the application of this information to the design of new and powerful inhibitors of disease-related enzymes, such as the HIV protease. In this overview, a few examples demonstrate the high potential of the QM/MM approach for sophisticated pharmaceutical compound design and supporting functions in the analysis of biomolecular structures.