Synthesis, X-ray crystallographic study and molecular docking of new α-sulfamidophosphonates: POM analyses of their cytotoxic activity

Discovery of new molecular hybrid derivatives with coumarin scaffold bearing pyrazole/oxadiazole moieties: Molecular docking, POM analyses, in silico pharmacokinetics and in vitro antimicrobial evaluation with identification of potent antitumor pharmacophore sites

This synthetic organic methodology involves the creation of novel coumarin-based hybrids of series (1-4) with pyrazole ring and (5-8) with oxadiazole moiety. The targeted compounds were tested for In vitro Antimicrobial efficacy against Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Candida albicans pathogenic microbes using disc diffusion and broth microdilution with ciprofloxacin and fluconazole as reference standards. Density functional theory (DFT) studies were used to study atomic structure and reactivity, including absolute electronegativity (χ), electrophilicity (ω), electron acceptor (ω+), donor capabilities (ω-), electron affinity (EA), energy gap (ΔE), global hardness (η), global softness (S), and ionisation potential (IP) and FMOs, NBOs, MEP, and Mulliken Charge analysis. The POM tests found three integrated pharmacophore sites with antibacterial, antiviral, and anticancer activities. Molecular docking studies are also used to determine the S. aureus nucleoside diphosphate kinase receptor's affinity and mode of action for the synthesized drugs. In silico analysis of thermodynamic and therapeutic effectiveness properties, including Lipinski's 'rule of five', Veber's rule, and ADME properties, predicted toxicity-free, non-carcinogenic, and risk-free oral administration of the synthesized complexes.

Anticancer activity, DFT study, ADMET prediction, and molecular docking of novel α-sulfamidophosphonates

A series of novel α-sulfamidophosphonate derivatives (3a-3 g) were synthesized and evaluated for anticancer activity against different human cancer cell lines (PRI, K562, and JURKAT). The antitumor activity of all compounds using the MTT test remains moderate compared to the standard drug chlorambucil. Compounds 3c and 3 g were found to be more active anticancer agent against PRI and K562 cells with IC50 value 0.056-0.097 and 0.182-0.133 mM, respectively. Molecular docking study related to binding affinity and binding mode analysis showed that synthesized compounds had potential to inhibit glutamate carboxypeptidase II (GCPII). Furthermore, computational analysis was performed through Density Functional Theory (DFT) utilizing the B3LYP 6-31 G (d, p) basis set and the theoretical results were correlated with experimental data. The ADME/toxicity analyses carried out by Swiss ADME and OSIRIS software show that all synthesized molecules exhibited good pharmacokinetics, bioavailability, and had no toxicity profile.

Ligand-Based Design of Novel Quinoline Derivatives as Potential Anticancer Agents: An In-Silico Virtual Screening Approach

In this study, using the Comparative Molecular Field Analysis (CoMFA) approach, the structure-activity relationship of 33 small quinoline-based compounds with biological anti-gastric cancer activity in vitro was analyzed in 3D space. Once the 3D geometric and energy structure of the target chemical library has been optimized and their steric and electrostatic molecular field descriptions computed, the ideal 3D-QSAR model is generated and matched using the Partial Least Squares regression (PLS) algorithm. The accuracy, statistical precision, and predictive power of the developed 3D-QSAR model were confirmed by a range of internal and external validations, which were interpreted by robust correlation coefficients (RTrain2=0.931; Qcv2=0.625; RTest2=0.875). After carefully analyzing the contour maps produced by the trained 3D-QSAR model, it was discovered that certain structural characteristics are beneficial for enhancing the anti-gastric cancer properties of Quinoline derivatives. Based on this information, a total of five new quinoline compounds were developed, with their biological activity improved and their drug-like bioavailability measured using POM calculations. To further explore the potential of these compounds, molecular docking and molecular dynamics simulations were performed in an aqueous environment for 100 nanoseconds, specifically targeting serine/threonine protein kinase. Overall, the new findings of this study can serve as a starting point for further experiments with a view to the identification and design of a potential next-generation drug for target therapy against cancer.

In Silico Pharmacokinetics, Molecular Docking and Molecular Dynamics Simulation Studies of Nucleoside Analogs for Drug Discovery- A Mini Review

Nucleoside analogs have been widely used as antiviral, antitumor, and antiparasitic agents due to their ability to inhibit nucleic acid synthesis. Adenosine, cytidine, guanosine, thymidine and uridine analogs such as didanosine, vidarabine, remdesivir, gemcitabine, lamivudine, acyclovir, abacavir, zidovusine, stavudine, and idoxuridine showed remarkable anticancer and antiviral activities. In our previously published articles, our main intention was to develop newer generation nucleoside analogs with acylation-induced modification of the hydroxyl group and showcase their biological potencies. In the process of developing nucleoside analogs, in silico studies play an important role and provide a scientific background for biological data. Molecular interactions between drugs and receptors followed by assessment of their stability in physiological environments, help to optimize the drug development process and minimize the burden of unwanted synthesis. Computational approaches, such as DFT, FMO, MEP, ADMET prediction, PASS prediction, POM analysis, molecular docking, and molecular dynamics simulation, are the most popular tools to culminate all preclinical study data and deliver a molecule with maximum bioactivity and minimum toxicity. Although clinical drug trials are crucial for providing dosage recommendations, they can only indirectly provide mechanistic information through researchers for pathological, physiological, and pharmacological determinants. As a result, in silico approaches are increasingly used in drug discovery and development to provide mechanistic information of clinical value. This article portrays the current status of these methods and highlights some remarkable contributions to the development of nucleoside analogs with optimized bioactivity.

Computer Analysis of the Inhibition of ACE2 by Flavonoids and Identification of Their Potential Antiviral Pharmacophore Site

In the present study, we investigated the antiviral activities of 17 flavonoids as natural products. These derivatives were evaluated for their in vitro antiviral activities against HIV and SARS-CoV-2. Their antiviral activity was evaluated for the first time based on POM (Petra/Osiris/Molispiration) theory and docking analysis. POM calculation was used to analyze the atomic charge and geometric characteristics. The side effects, drug similarities, and drug scores were also assumed for the stable structure of each compound. These results correlated with the experimental values. The bioinformatics POM analyses of the relative antiviral activities of these derivatives are reported for the first time.

Investigation of the dual role of acyl phloroglucinols as a new hope for antibacterial and anti-SARS-CoV-2 agents employing integrated in vitro and multi-phase in silico approaches

With the rapid spread of multi-drug-resistant bacteria and more infectious or aggressive variants of SARS-CoV-2, it is critical to develop drugs that can quickly adapt to evolving bacterial and viral mutations. In this study, encouraged by nature, we synthesized a series of phloroglucinol (PG) derivatives, acyl phloroglucinols (ACPLs) 2a-4c by mimicking the structure of the natural antifungal 2,4-diacetylphloroglucinol 3a (2,4-DAPG). According to the quantum chemical calculation, these compounds were expected to be exceptionally favourable for intermolecular interaction with protein receptors. Intriguingly, the in vitro study of Staphylococcus aureus (S. aureus) ATCC 25923 and Escherichia coli (E. coli) ATCC 25922, showed that the four ACPLs 3a-4a had good antibacterial activity and selectivity against gram-positive bacteria, S. aureus. These results were then supported by in silico molecular docking and molecular dynamics simulations (MDs) between these potent compounds and the S. aureus FtsA protein (PDB ID: 3WQU). Furthermore, with the aid of the knowledge base Virus-CKB along with the molecular docking study, it was found that the three ACPLs 4a-4c showed potential inhibitors against SARS-CoV-2 PLpro (PDB ID: 7CMD). Additionally, 100 ns of MDs was carried out in order to assess the stability behaviour of ACPLs at the docked site. Moreover, in silico ADME/T and drug likeness of all studied ACPLs were also predicted. Finally, shape-based screening of FDA-approved drugs was performed using the most prominent synthesized ACPLs as a template, enabling us to include several medications that could be utilized as antibacterial and antiviral drug candidates.Communicated by Ramaswamy H. Sarma.

Synthesis, antimicrobial, SAR, PASS, molecular docking, molecular dynamics and pharmacokinetics studies of 5'-O-uridine derivatives bearing acyl moieties: POM study and identification of the pharmacophore sites

Because of their superior antibacterial and pharmacokinetic capabilities, many nucleoside-based esters show potential against microorganisms, and may be used as pharmacological agents to address multidrug-resistant pathogenic problems. In this study, several aliphatic and aromatic groups were inserted to synthesize various 5'-O-decanoyluridine (2-5) and 5'-O-lauroyluridine derivatives (6-7) for antimicrobial, in silico computational, pharmacokinetic and POM (Petra/Osiris/Molinspiration). The chemical structures of the synthesized uridine derivatives were confirmed by physicochemical, elemental, and spectroscopic analyses. In vitro antimicrobial screening against five bacteria and two fungi, as well as the prediction of substance activity spectra (PASS), revealed that these uridine derivatives have promising antifungal properties when compared to the antibacterial activities. Density functional theory (DFT) was used to calculate the thermodynamic and physicochemical properties. Molecular docking was conducted against lanosterol 14a-demethylase CYP51A1 (3JUV) and Aspergillus flavus (1R4U) and revealed binding affinities and non-covalent interactions with the target. Then, a 150 ns molecular dynamic simulation was performed to confirm the behavior of the complex structure formed by microbial protein under in silico physiological conditions to examine its stability over time, which revealed a stable conformation and binding pattern in a stimulating environment of uridine derivatives. The acyl chain {CH₃(CH₂)₉CO-} and {CH₃(CH₂)₁₀CO-} in conjunction with sugar, was determined to have the most potent activity against bacterial and fungal pathogens in a structure-activity relationships (SAR) investigation. POM analyses were conducted with the presence of an antifungal (O ^δ- -- O' ^δ-) pharmacophore site. Overall, the present study might be useful for the development of uridine-based novel multidrug-resistant antimicrobial.

A pair of carbazate derivatives as novel Schiff base ligands: DFT and POM theory supported spectroscopic and biological evaluation

Schiff bases are mentioned as strongly important molecular scaffolds of industrial and medicinal purposes. Due to wide range applications of carbazate derivatives herein synthesis and characterization of a new Schiff base ligand, (E)-ethyl 2-(4-methoxybenzylidene)hydrazinecarboxylate and 4-(nitrobenzaldehyde)ethylcarbazate are reported. The compound was characterized on the basis of experimental and density functional theory calculations (using the B3LYP and 6-31 G(d,p)formalism combination). Among characterization techniques elemental analysis, FT-IR, UV-Vis and NMR spectroscopic evaluations were mainly employed to carry out the formulation of the compound. In addition to computational validation of characterization other significant molecular parameters were also evaluated including geometry optimization, frontier molecular orbital analysis (FMO) and Columbic interaction of different constituent atoms of the title compound. A good agreement has been found between DFT and experimental outcomes confined to prove the structure of the compound. Moreover, molecular docking and antimicrobial studies have proven the Schiff base as an effective bioactive compound.Communicated by Ramaswamy H. Sarma.

Synthesis, in silico study (DFT, ADMET) and crystal structure of novel sulfamoyloxy-oxazolidinones: Interaction with SARS-CoV-2

A new series of sulfamoyloxyoxazolidinone (SOO) derivatives have been synthesized and characterized by single-crystal X-ray diffraction, NMR, IR, MS and EA. Chemical reactivity and geometrical characteristics of the target compounds were investigated using DFT method. The possible binding mode between SOO and Main protease (Mpro) of SARS-CoV-2 and their reactivity were studied using molecular docking simulation. Single crystal X-ray diffraction showed that SOO crystallizes in a monoclinic system with P 2 1 space group. The binding energy of the SARS-CoV-2/Mpro-SOO complex and the calculated inhibition constant using docking simulation showed that the active SOO molecule has the ability to inhibit SARS-CoV2. We studied the prediction of absorption, distribution, properties of metabolism, excretion and toxicity (ADMET) of the synthesized molecules.

Efficient synthesis and antitumor activity of novel oxazaphosphinane derivatives: X-ray crystallography, DFT study and molecular docking

A novel potentially biologically active oxazaphosphinane derivatives was synthesized by facile synthetic approaches from the combination of hydroxyaniline, aldehyde, and triethylphosphite. The crystal structure of compound 1b has been determined. Single crystals belong to the triclinic system with p - 1 space. The relative in vitro antitumor activity against human cell lines (PRI, K562, and JURKAT) of these derivatives in comparison to chlorombucil is reported. All synthesized compound showed excellent activity with IC50 value of 0.014-0.035 mM. The binding energy of the Epidermal growth factor receptor (EGFR)-oxazaphosphinane complex and the calculated inhibition constant using docking simulation showed that all molecules has the ability to inhibit EGFR therapeutic target. In addition, DFT calculation has been used to analyze the electronic and geometric characteristics.

In vitro potential antiviral SARS-CoV-19- activity of natural product thymohydroquinone and dithymoquinone from Nigella sativa

Inflammation, oxidation, and compromised immunity all increase the dangers of COVID-19, whereas many pharmaceutical protocols may lead to increased immunity such as ingesting from sources containing vitamin E and zinc. A global search for natural remedies to fight COVID-19 has emerged, to assist in the treatment of this infamous coronavirus. Nigella satvia is a world-renowned plant, an esteemed herbal remedy, which can be used as a liquid medicine to increase immunity while decreasing the dangers of acute respiratory distress syndrome. Thymoqinone (TQ), dithymoqinone (DTQ) and thymohydroquinone (THQ), are major compounds of the essential oil contained in N.sativa. A current study aims to discover the antiviral activity of two compounds, Thymohydroquinone and Dithymoquinone, which are synthesized through simple chemical procedures, deriving from thymoquinone, which happens to be a major compound of Nigella sativa. A half-maximal cytotoxic concentration, "CC50", was calculated by MTT assay for each individual drug, The sample showed anti-SARS-CoV-2 activity at non-cytotoxic nanomolar concentrations in vitro with a low selectivity index (CC50/IC50 = 31.74/23.15 = 1.4), whereby Dimthymoquinone shows high cytotoxicity.

In silico evaluation of molecular interactions between macrocyclic inhibitors with the HCV NS3 protease. Docking and identification of antiviral pharmacophore site

An array of computational approaches DFT/QSAR/POM methods has been used for a better understanding of drug properties regarding 13 inhibitor derivatives containing either P2 cyclopentane P1 carboxylic acid moiety (1-9) or a P1 cyclopropyl acyl sulfonamide (10-13). To further recognize binding interactions and their activity trends, molecular docking studies were carried out with the use of HCV, which can be used to accurately predict the interactions of ligands with the receptor. The QSAR models are developed through the use of Multiple Linear Regression (MLR) together with Principal Component Analysis (PCA) methods. The statistical results indicate the multiple correlation coefficient R² = 0.840, which shows favorable estimation stability, as well as showing a significant correlation between the HCV NS3 protease of the studied compounds and their electron-accepting ability. The POM analysis of the Physico-chemical properties of compounds 1-13, shows that they are bearing (O1, O2) and/or (O1, O2, O3) antiviral pockets, whereby all oxygen atoms are Osp2 and bearing negative charges. Similar to the reference ligand (F9K), the most active compound 10 was bound deeply into the binding cavity of NS3 protease making interactions with the residues Gly137, His57, Ala157, and His528. The anti-hepatitis pharmacophore site is similar to the anti-HIV pharmacophore site.

How to face COVID-19: proposed treatments based on remdesivir and hydroxychloroquine in the presence of zinc sulfate. Docking/DFT/POM structural analysis

Remdesivir and hydroxychloroquine derivatives form two important classes of heterocyclic compounds. They are known for their anti-malarial biological activity. This research aims to analyze the physicochemical properties of remdesivir and hydroxychloroquine compounds by the computational approach. DFT, docking, and POM analyses also identify antiviral pharmacophore sites of both compounds. The antiviral activity of hydroxychloroquine compound's in the presence of zinc sulfate and azithromycin is evaluated through its capacity to coordinate transition metals (M = Cu, Ni, Zn, Co, Ru, Pt). The obtained bioinformatic results showed the potent antiviral/antibacterial activity of the prepared mixture (Hydroxychloroquine/Azithromycin/Zinc sulfate) for all the opportunistic Gram-positive, Gram-negative in the presence of coronavirus compared with the complexes Polypyridine-Ruthenium-di-aquo. The postulated zinc(II) complex of hydroxychloroquine derivatives are indeed an effective antibacterial and antiviral agent against coronavirus and should be extended to other pathogens. The combination of a pharmacophore site with a redox [Metal(OH₂)₂] moiety is of crucial role to fight against viruses and bacteria strains. [Formula: see text]Communicated by Ramaswamy H. Sarma.

Synthesis, biological activity and POM/DFT/docking analyses of annulated pyrano[2,3-d]pyrimidine derivatives: Identification of antibacterial and antitumor pharmacophore sites

New annulated pyrano[2,3-d]pyrimidine derivatives were synthesized with hydroxyl, methoxy, bromine, nitrile and nitro substituents on its skeleton. The correlated electronic effect of substituents on the magnitude of antibacterial activity was noted. The electron donating substituents (namely; 4-OH, 4-OCH₃, 4-Br) and electron withdrawing substituents (4-NO₂) on phenyl ring in the pyrano[2,3-d]pyrimidine skeleton exerted different influence on its antimicrobial activity against some Gram-positive and Gram-negative bacteria such as Pseudomonas aureus, E. coli, Staphylococcus aureus, Klebsiella pneumonia and Bacillus cereus. All the pyrano[2,3-d]pyrimidines were characterized by spectroscopic analyses. Antibacterial screening revealed that the presence of heteroaryl, cyano and amino groups on pyrano[2,3-d]pyrimidine skeleton increases its penetrating power on the bacterial cell wall so that the product becomes more biologically active. So the the nature of electron withdrawing or electro-donnor Impact of substituents should be taken in consideration in drug design. Hydrolysis of -CRN to amide restored vital Intramolecular interaction like ortho-nitrophenyl and ONO^δ-…NH^δ+/amide link, offering a crucial template for antibacterial NH, HO-pharmacophore sites, which ultimately elevated innate antimicrobial profiles. POM combinatorial analysis of tangible electronic contributions due to armed annulated pyrano[2,3-d]pyrimidines concluded their broad antimicrobial activity and viable/prominent drug score index through perspective parameters particularly: inter atomic distance/linkers, steric, electronic, polar parameters, and with a different polarising effect of electron donating/withdrawing environments of substituents. Furthermore, an anti-Kinase pharmacophore site (OCNHCO) was evaluated in continuation of the POM investigations. All synthesized products verified fewer side effects than standard streptomycin, but facile implication in selective cancer media (viz. breast or leucemia still needs to be screened).

DFT calculations and POM analyses of cytotoxicity of some flavonoids from aerial parts of Cupressus sempervirens: Docking and identification of pharmacophore sites

Two known polyphenols named apigenin 7-O-β-d-glucopyranoside (S1) and querctine-3-O-glucoside (S2), along with another two new compounds apigenin 4'-geranyl-8-glucopyranosyl-7-O-α-glucopyranoside (S3) and apigenin 4'-pernyl-8-glucopyranosyl -7-O-α-glucopyranoside (S4), were isolated from the leaves of Cupressus sempervirens. Structure elucidation of the isolated polyphenols was established on the basis of detailed spectroscopic analysis like 1D and 2D NMR analyses including ¹H NMR, ¹³C NMR, COSY, DEPT, HMQC, UV, and Electron Spray Ionization Mass Spectroscopy (ESI-MS). Density Functional Theory (DFT) of computational, Petra/Osiris/Molinspiration (POM), and docking analyses methods were applied in the structural validation of new isolated compounds. The isolated compounds S1-S4 showed significant cytotoxicity against human hepatocellular liver carcinoma HepG2 cells, MCF-7, HC116 and A549.