New thiophene-derived α-aminophosphonic acids: Synthesis under microwave irradiations, antioxidant and antifungal activities, DFT investigations and SARS-CoV-2 main protease inhibition

Comprehensive biochemical, molecular and structural characterization of subtilisin with fibrinolytic potential in bioprocessing

Enzyme deployment is proliferating extensively in industries owing to their environmentally friendly and easily degradable attributes. This article undertakes an exhaustive examination of wild subtilisin enzyme, covering purification, biochemical delineation, analytical techniques, and practical implementations. The purification methodology involved partial refinement, anionic exchange, and gel filtration chromatography, culminating in a purification factor of 3.406, corroborated by SDS-PAGE showcasing a molecular weight of ~ 42 kDa. Biochemical scrutiny unveiled the enzyme's response, with an optimal pH at 9 and temperature peak at 60 ℃. Various surfactants, metal ions, organic solvents and inhibitors exhibited notable efficacy. Substrate specificity and kinetics showcased the utmost specificity with N-Suc-F-A-A-F-pNA, registering Km and Vmax values of 0.731 ± 0.5 mM and 0.87 ± 9 × 103 U/mg, respectively. Different bioanalytical techniquesproffered insights into structural and biophysical facets. Practical applications encompassed goat skin depilation, feather disintegration, blood clot dissolution, exemplifying the enzyme's multifaceted utility. To embark upon the elucidation of structure-function relationships, a three-dimensional model was devised through homology modelling, leveraging existing subtilisin structures (PDB: 3WHI). Molecular docking score of - 8.8 kcal/mol and dynamic simulations augmented the comprehension of molecular interactions with N-Suc-F-A-A-F-pNA. This research significantly contributes to unravelling the biochemical intricacies of wild subtilisin and underscores potential industrial and biomedical prowess. Subtilisin can be explored for its thrombolytic potential in several cardiovascular diseases. It may aid in the management of thrombosis by dissolving blood clots in conditions like deep pulmonary embolism, myocardial infarction, ischemic strokes, and in atherosclerosis by breaking down fibrin in arterial plaques, thus preventing heart attacks and strokes.

Development of new benzil-hydrazone derivatives as anticholinesterase inhibitors: synthesis, X-ray analysis, DFT study and in vitro/in silico evaluation

Alzheimer's disease (AD) is a complex neurodegenerative disorder affecting the central nervous system. Current drugs for AD have limited effectiveness and often come with side effects. Consequently, there is a pressing need to develop new, safe, and more effective treatments for Alzheimer's disease. In this work, two novel benzil-hydrazone compounds, abbreviated 2-ClMHB and 2-ClBHB, were synthesized for the first time by refluxing the benzil with 2-Chloro phenyl hydrazine and they have been tested for their in vitro anti-cholinesterase activities and in silico acetyl and butyryl enzymes inhibition. The resulting products were characterized using UV-Vis and IR spectroscopy, while the single-crystal X-ray diffraction investigation was successful in establishing the structures of these compounds. DFT calculations have been successfully made to correlate the experimental data. According to biological studies, the synthesized hydrazones significantly inhibited both butyrylcholinesterase (2-ClMHB: 20.95 ± 1.29 µM and 2-ClBHB: 31.21 ± 1.50 µM) and acetylcholinesterase (2-ClMHB: 21.80 ± 1.10 µM and 2-ClBHB: 10.38 ± 1.27 µM). Moreover, molecular docking was also employed to locate the molecule with the optimum interaction and stability as well as to explain the experimental findings. The compound's dynamic nature, binding interaction, and protein-ligand stability were investigated using molecular dynamics (MD) simulations. Analyzing parameters such as RMSD and RMSF indicated that the compound remained stable throughout the 100 ns MD simulation. Finally, the drugs displayed high oral bioavailability, as per projected ADME and pharmacokinetic parameters.

Exploring Thiophene Derivatives: Synthesis Strategies and Biological Significance

OBJECTIVES

Thiophene is one of the most important heterocyclic scaffolds with notable pharmacological properties. Thiophene and its derivatives are of particular interest among sulphurcontaining heterocycles because of their similarities to numerous natural and synthetic compounds with identified potential. The purpose of this study is to extensively analyse the synthetic pathways adopted for synthesising thiophene derivatives and investigate their various biological functions.

METHODS

A comprehensive review of the existing literature was conducted to collect data pertaining to the methods that are employed for the synthesis of thiophene derivatives. A comprehensive search was carried out through relevant databases, including work published in 2024. A variety of synthesis procedures were identified and arranged, encompassing both traditional approaches like the Gewald reaction and contemporary ones like microwave-assisted synthesis and green synthesis. In addition, a comprehensive compilation of in vitro and in vivo studies was conducted to investigate the biological effects of 50 distinct thiophene derivatives. The primary focus of the studies was on various activities such as anti-cancer, anti-inflammatory, antiprotozoal, antibacterial, antioxidant, and antiviral functions.

RESULTS

Diverse methodologies have been employed in the synthesis of thiophene derivatives, encompassing both conventional and modern methods. Furthermore, the biological potential of thiophene derivatives was investigated, demonstrating a broad range of actions. Key structural elements necessary for biological activity were clarified by investigations of the structure-activity relationship.

CONCLUSION

The biological potential and flexible synthesis pathways of thiophene derivatives make them attractive candidates for use in medicinal and pharmaceutical chemistry. Understanding the different synthesis methods and biological actions of thiophene derivatives may assist rational design and create novel treatments for a variety of conditions. The potential for these compounds to be further explored and optimised is considerable for the next drug development initiatives.

Design, Synthesis, Biological Evaluation and Molecular Docking Studies of New Thiazolidinone Derivatives as NNRTIs and SARS-CoV-2 Main Protease Inhibitors

HIV-1 remains a major health problem worldwide since the virus has developed drug-resistant strains, so, the need for novel agents is urgent. The protein reverse transcriptase plays fundamental role in the viruses' replication cycle. FDA approved Delavirdine bearing a sulfonamide moiety, while thiazolidinone has demonstrated significant anti-HIV activity as a core heterocycle or derivative of substituted heterocycles. In this study, thirty new thiazolidinone derivatives (series A, B and C) bearing sulfonamide group were designed, synthesized and evaluated for their HIV-1 RT inhibition activity predicted by computer program PASS taking into account the best features of available NNRTIs as well as against SARS-COV-2 main protease. Seven compounds showed good anti-HIV inhibitory activity, with two of them, C1 and C2 being better (IC50 0.18 μΜ & 0.12 μΜ respectively) than the reference drug nevirapine (IC50 0.31 μΜ). The evaluation of molecules to inhibit the main protease revealed that 6 of the synthesized compounds exhibited excellent to moderate activity with two of them (B4 and B10) having better IC50 values (0.15 & 0.19 μΜ respectively) than the reference inhibitor GC376 (IC50 0.439 μΜ). The docking studies is coincides with experimental results, showing good binding mode to both enzymes.

8-Aminoquinoline derived two Schiff base platforms: Synthesis, characterization, DFT insights, corrosion inhibitor, molecular docking, and pH-dependent antibacterial study

The current research divulges the synthesis of two new Schiff base (SB) (L NAPH /L O-VAN ) derived from 8-aminoquinoline (8-AMQ) in the presence of 2-hydroxy naphthaldehyde (NAPH) and ortho-vanillin (O-VAN) in CH3OH solvent. They are structurally characterized by spectroscopic methods (IR/Raman/UV-vis/DRS/NMR) and SEM-EDX. SB compounds have a biologically active avenue of azomethine/imine group (H-C=N) that can donate N e's to Mn + ions, showing coordinating flexibility. The -OH and imine (H-C=N) groups are stable in air, light, and alkalis but undergo acidic environments hydrolysis, separating -NH2 and carbonyl compounds. Moreover, buffer solutions with a pH range of 4-6 release aldehyde. Molecular electrostatic potential (MEP), Frontier molecular orbitals (FMO), Fukui function, and Non-linear optical (NLO) were conducted to elucidate SBs chemical potency, optoelectronic significance, and corrosion inhibitor. Accordingly, the calculated ΔE of FMO for L NAPH and L O-VAN is 3.82 and 4.08 eV, ensuring potent biological function. DFT supported the experimental and theoretical IR spectral correlation to enrich better structural insights. NLO-based polarizability (α) and hyperpolarizability (β) factors successfully explore the potential optoelectronic significance. Molecular docking experiments were simulated against DNA, anti-COVID-19, and E. coli. The potential microbiological activity was screened against the bacterial strains E. coli, Klebsiella, Bacillus, and Pseudomonas sp. based on zone of inhibition and MIC values. These experiments also explored the fact that L NAPH and L O-VAN discourage microbial cell biofilms and corrosion. We extensively covered the as-prepared compounds' pH-dependent bacterial effects.

Synthesis, Theoretical, in Silico and in Vitro Biological Evaluation Studies of New Thiosemicarbazones as Enzyme Inhibitors

Eleven new thiosemicarbazone derivatives (1-11) were designed from nine different biologically and pharmacologically important isothiocyanate derivatives containing functional groups such as fluorine, chlorine, methoxy, methyl, and nitro at various positions of the phenyl ring, in addition to the benzyl unit in the molecular skeletal structure. First, their substituted-thiosemicarbazide derivatives were synthesized from the treatment of isothiocyanate with hydrazine to synthesize the designed compounds. Through a one-step easy synthesis and an eco-friendly process, the designed compounds were synthesized with yields of up to 95 % from the treatment of the thiosemicarbazides with aldehyde derivatives having methoxy and hydroxy groups. The structures of the synthesized molecules were elucidated with elemental analysis and FT-IR, 1 H-NMR, and 13 C-NMR spectroscopic methods. The electronic and spectroscopic properties of the compounds were determined by the DFT calculations performed at the B3LYP/6-311++G(2d,2p) level of theory, and the experimental findings were supported. The effects of some global reactivity parameters and nucleophilic-electrophilic attack abilities of the compounds on the enzyme inhibition properties were also investigated. They exhibited a highly potent inhibition effect on acetylcholinesterase (AChE) and carbonic anhydrases (hCAs) (KI values are in the range of 23.54±4.34 to 185.90±26.16 nM, 103.90±23.49 to 325.90±77.99 nM, and 86.15±18.58 to 287.70±43.09 nM for AChE, hCA I, and hCA II, respectively). Furthermore, molecular docking simulations were performed to explain each enzyme-ligand complex's interaction.

Various Biomimetics, Including Peptides as Antifungals

Biomimetics, which are similar to natural compounds that play an important role in the metabolism, manifestation of functional activity and reproduction of various fungi, have a pronounced attraction in the current search for new effective antifungals. Actual trends in the development of this area of research indicate that unnatural amino acids can be used as such biomimetics, including those containing halogen atoms; compounds similar to nitrogenous bases embedded in the nucleic acids synthesized by fungi; peptides imitating fungal analogs; molecules similar to natural substrates of numerous fungal enzymes and quorum-sensing signaling molecules of fungi and yeast, etc. Most parts of this review are devoted to the analysis of semi-synthetic and synthetic antifungal peptides and their targets of action. This review is aimed at combining and systematizing the current scientific information accumulating in this area of research, developing various antifungals with an assessment of the effectiveness of the created biomimetics and the possibility of combining them with other antimicrobial substances to reduce cell resistance and improve antifungal effects.

New bi-phosphonate derivative: Synthesis, characterization, antioxidant activity in vitro and via cyclic voltammetry mode and evaluation of its inhibition of SARS-CoV-2 main protease

In this study, we have synthesized a new molecule labeled HBPA. Its molecular structure was determined by spectroscopic methods such as: FT-IR, NMR (¹H, ¹³C and ³¹P); our compound is subjected to two antioxidant activities assays: DPPH scavenging and ferric reducing antioxidant power (FRAP); in the results, HBPA was expanded remarkable inhibition when compared especially to standard BHT with values of 14.936±0.808 and 7.1486±0.0645 μg/ml, respectively; in addition to the scavenging test of superoxide anion integrated in electrochemical process, it elucidated a strongly stable interaction towards the radical by evaluating the thermodynamic descriptors (Gibbs free energy ΔG° and the binding constant K_b). Besides, the electrochemical behavior of HBPA was distinguished by an irreversible system and for the electrochemical regime adopted at the surface of the electrode; a diffusion governed by a slow charge transfer was deduced. The molecular docking of HBPA was conducted beside Chloroquine and the obtained results were indicated a significant binding with active sites of the SARS-CoV-2 main protease (M^pro).

Transdermal Delivery of α-Aminophosphonates as Semisolid Formulations-An In Vitro-Ex Vivo Study

α-Aminophosphonates are organophosphorus compounds with an obvious similarity with α-amino acids. Owing to their biological and pharmacological characteristics, they have attracted the attention of many medicinal chemists. α-Aminophosphonates are known to exhibit antiviral, antitumor, antimicrobial, antioxidant and antibacterial activities, which can all be important in pathological dermatological conditions. However, their ADMET properties are not well studied. The aim of the current study was to provide preliminary information about the skin penetration of three preselected α-aminophosphonates when applying them as topical cream formulations in static and dynamic diffusion chambers. The results indicate that aminophosphonate 1a, without any substituent in the para position, shows the best release from the formulation and the highest absorption through the excised skin. However, based on our previous study, the in vitro pharmacological potency was higher in the case of para-substituted molecules 1b and 1c. The particle size and rheological studies revealed that the 2% cream of aminophosphonate 1a was the most homogenous formulation. In conclusion, the most promising molecule was 1a, but further experiments are proposed to uncover the possible transporter interactions in the skin, optimize the topical formulations and improve PK/PD profiles in case of transdermal delivery.

A novel coumarin-triazole-thiophene hybrid: synthesis, characterization, ADMET prediction, molecular docking and molecular dynamics studies with a series of SARS-CoV-2 proteins

Synthesis, characterization and theoretical studies of a novel coumarin-triazole-thiophene hybrid 4-(((4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazol-3-yl)thio)methyl)-6,7-dimethyl-2H-chromen-2-one (1), which was fabricated from 4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazole-3-thiol and 4-(chloromethyl)-6,7-dimethyl-2H-chromen-2-one, are reported. The resulting compound was characterized by microanalysis, IR, 1H, and 13C APT NMR spectroscopy. The DFT calculations examined the structure and electronic properties of 1 in gas phase. Its reactivity descriptors and molecular electrostatic potential revealed the reactivity and the reactive centers of 1. ADMET properties of 1 were evaluated using the respective online tools. It was established that 1 exhibit positive gastrointestinal absorption properties and negative human blood-brain barrier penetration. The Toxicity Model Report revealed that 1 belongs to toxicity class 4. Molecular docking was additionally applied to study the interaction of 1 with some SARS-CoV-2 proteins. It was established that the title compound is active against all the applied proteins with the most efficient interaction with Papain-like protease (PLpro). The interaction of 1 with the applied proteins was also studied using molecular dynamics simulations.

Graphical abstract

A novel coumarin-triazole-thiophene hybrid 4-(((4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazol-3-yl)thio)methyl)-6,7-dimethyl-2H-chromen-2-one (1) is reported. The structure and electronic properties of 1 were examined by the DFT calculations. ADMET properties of 1 were also evaluated. Molecular docking and molecular dynamics simulations were applied to study interactions of 1 with a series of the SARS-CoV-2 proteins.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12039-022-02127-0.

X-ray Structure Determination of Naphthalen-2-yl 1-(Benzamido(diethoxyphosphoryl)methyl)-1H-1,2,3-triazole-4-carboxylate

We have previously published on a new triazolic phosphonic α-amino ester in position 4 on the triazole ring of a naphthalene ester. The aim of the present paper was to describe its crystallographic study by XRD. The crystal structure of naphthalen-2-yl 1-(benzamido(diethoxyphosphoryl)methyl)-1H-1,2,3-triazole-4-carboxylate was determined by single-crystal X-ray diffraction. This compound crystallizes in the monoclinic system, space group P21/c. The naphthalene system is almost planar and makes dihedral angles of 67.1(2)° and 63.9(2)° with the triazole ring and the phenyl cycle, respectively. The phosphorus atom is surrounded by three oxygen atoms and one carbon atom building a distorted tetrahedron. It is also noted, that one of the two ethyl groups is disordered. In the crystal, the molecules are connected through C-H…O and N-H…O hydrogen bonds to build dimers that are linked together by C-H…O hydrogen bonds, in addition to C-H…π interactions. The presence of an intramolecular hydrogen bond contributes to the stability of the molecular conformation by completing the S(5) cycle.