Target-based drug discovery, ADMET profiling and bioactivity studies of antibiotics as potential inhibitors of SARS-CoV-2 main protease (Mpro)

Theoretical investigations of some isolated compounds from Calophyllum flavoramulum as potential antioxidant agents and inhibitors of AGEs

In this paper, we have attempted a theoretical calculation of some plant-isolated compounds as potential inhibitors of oxidative stress and Advanced Glycation Endproducts (AGEs). Herein, theoretical reactivity indices based on the CDFT theory were computed to explore the reactivity of five isolated products from Calophyllum flavoramulum. Global reactivity indices based on HOMO and LUMO energy such as electronic chemical potential, hardness, electrophilicity and the local reactivity descriptors Parr function, molecular electrostatic potentials(MEP), electrostatic potential (ESP) and thermodynamic parameters for the studied compounds are computed and discussed using DFT method and two functionals B3LYP and CAM-B3LYP with 6-31 G(d,p) basis set. The free radical scavenging activity mechanisms (HAT, SET-PT, and SPLET) of some of the isolated products with DPPH are also presented in this work. SET-PT mechanism of the antiradical activity is found to be thermodynamically favorable. Furthermore, a molecular docking study with RAGE receptor and AtGSTF2 enzyme was conducted, in which flavonoids 4 and 5 show a low binding affinity with -8.42 and -10.49 kcal/mol for RAGE, -8.67 and -9.00 kcal/mol for AtGSTF2. After the encouraging outcomes from the molecular docking study, the 4-AtGSTF2 and 5-RAGE complex were subjected to 200 ns molecular dynamics simulation using Desmond, where both studied systems exhibited remarkable stability throughout the 200 ns simulations. Also, the MM-GBSA method was measured by calculating the binding free energy using the individual energy components. Finally, the ADMET predictions were assessed to anticipate the behavior of a drug candidate within the human body.

Zinc(II) coordination compound with N'-(pyridin-2-ylmethylene)nicotinohydrazide: Synthesis, crystal structure, computational and cytotoxicity studies

In this work, we report on the synthesis of a novel zinc(II) coordination compound [ZnL2] (1), which was readily obtained from the reaction of Zn(OAc)·2H2O and N'-(pyridin-2-ylmethylene)nicotinohydrazide (HL) in methanol. Recrystallization of 1 from dimethylformamide under ambient conditions allowed to produce yellow block-like crystals of 1·H2O. Complex 1·H2O was characterized by FT-IR and 1H NMR spectroscopy, while its optical properties were studied by UV-vis and spectrofluorimetry in methanol. The crystal structure of the title complex was revealed by single crystal X-ray diffraction and further explored in detail by the Hirshfeld surface analysis. Theoretical investigations based on the DFT calculations have also been applied to show the electronic properties of complex 1. The antitumor activities of the parent ligand HL and complex 1 were studied using Dalton's lymphoma malignant cancer model. Both compounds were found to induce concentration-dependent cytotoxicity and apoptotic cell death, leading to a decrease in cell viability, body weight, and tumor volume in mice with the superior activity of complex 1 over HL. Mice treated with complex 1 demonstrated an increase in life span with a survival period of 23 days. Finally, using a molecular docking approach, we have probed complex 1 to inhibit the recombinant mouse tumor-necrosis factor alpha (mTNF).

Antibacterial activities, PASS prediction and ADME analysis of phytochemicals from Curcubita moschata, Curcubita maxima, and Irvingia gabonensis: insights from in silico studies

Microbial infection management and treatment are crucial as a result of the prevalent antimicrobial resistance issue. Progressive studies are being carried out on how to develop drugs that can mitigate the resistance trends of these microorganisms. Secondary metabolites of plants can also be employed and accessed for this role, as the current study examines the antibacterial activities of phytochemicals from three (3) plants (Cucubita moschata, Cucubita maxima, and Irvingia gabonesis) through computational approaches. Molecular docking studies were carried out to show the binding affinities of the phytochemicals against two target receptors (DNA gyrase and Penicillin Binding Protein 3). In addition, drug likeness analysis, bioactivity and oral-bioavailability properties, absorption, distribution, metabolism, and excretion (ADME) profiling, as well as prediction of activity spectra for substances (PASS) using online tools like SwissADME, PASS online, AdmetSAR2, and Discovery Studio, were also performed. The results obtained identified isochlorogenic acid and apigenin-7-O-glucoside for DNA gyrase (1KZN) and apigenin-7-O-glucoside for Penicillin Binding Protein 3 (4BJP), which were further subjected to molecular dynamics simulation (MDS) and therefore recommended as the lead compounds.

Analysing potent biomarkers along phytochemicals for breast cancer therapy: an in silico approach

PURPOSE

This research focused on the identification of herbal compounds as potential anti-cancer drugs, especially for breast cancer, that involved the recognition of Notch downstream targets NOTCH proteins (1-4) specifically expressed in breast tumours as biomarkers for prognosis, along with P53 tumour antigens, that were used as comparisons to check the sensitivity of the herbal bio-compounds.

METHODS

After investigating phytochemical candidates, we employed an approach for computer-aided drug design and analysis to find strong breast cancer inhibitors. The present study utilized in silico analyses and protein docking techniques to characterize and rank selected bio-compounds for their efficiency in oncogenic inhibition for use in precise carcinomic cell growth control.

RESULTS

Several of the identified phytocompounds found in herbs followed Lipinski's Rule of Five and could be further investigated as potential medicinal molecules. Based on the Vina score obtained after the docking process, the active compound Epigallocatechin gallate in green tea with NOTCH (1-4) and P53 proteins showed promising results for future drug repurposing. The stiffness and binding stability of green tea pharmacological complexes were further elucidated by the molecular dynamic simulations carried out for the highest scoring phytochemical ligand complex.

CONCLUSION

The target-ligand complex of green tea active compound Epigallocatechin gallate with NOTCH (1-4) had the potential to become potent anti-breast cancer therapeutic candidates following further research involving wet-lab experiments.

Diabetic wound healing of aloe vera major phytoconstituents through TGF-β1 suppression via in-silico docking, molecular dynamic simulation and pharmacokinetic studies

To restore the integrity of the skin and subcutaneous tissue, the wound healing process involves a complex series of well-orchestrated biochemical and cellular events. Due to the existence of various active components, accessibility and few side effects, some plant extracts and their phytoconstituents are recognised as viable options for wound healing agents. To find possible inhibitors of diabetic wound healing, four main constituents of aloe vera were identified from the literature. TGF-β1 and the compounds were studied using molecular docking to see how they interacted with the active site of target protein (PDB ID: 6B8Y). The pharmacokinetics investigation of the aloe emodin with the highest dock score complied with all the Lipinski's rule of five and pharmacokinetics criteria. Conformational change in the docked complex of Aloe emodin was investigated with the Amber simulation software, via a molecular dynamic (MD) simulation. The MD simulations of aloe emodin bound to TGF-β1 showed the significant structural rotations and twists occurring from 0 to 200 ns. The estimate of the aloe emodin-TGF-β1 complex's binding free energy has also been done using MM-PBSA/GBSA techniques. Additionally, aloe emodin has a wide range of enzymatic activities since their probability active (Pa) values is >0.700. 'Aloe emodin', an active extract of aloe vera, has been identified as the key chemical in the current investigation that can inhibit diabetic wound healing. Both in-vitro and in-vivo experiments will be used in a wet lab to confirm the current computational findings.Communicated by Ramaswamy H. Sarma.

Eco-Friendly Synthesis of 1H-benzo[d]imidazole Derivatives by ZnO NPs Characterization, DFT Studies, Antioxidant and Insilico Studies

Benzimidazoles are classified as a category of heterocyclic compounds. Molecules having benzimidazole motifs show promising utility in organic and scientific studies. A series of mono-substituted benzimidazoles were synthesized by ZnO-NPs via cyclocondensation between substituted aromatic aldehydes and o-phenylene diamine. The synthesized compounds were characterized and compared with the traditional methods. The nano-catalyzed method displayed a higher yield, shorter time and recyclable catalyst. The DFT study and antioxidant activity were investigated for benzo[d]imidazole derivatives. Compound 2a exhibited the highest antioxidant activity among the tested compounds. We focused on the catalytic activity of ZnO in the synthesis of heterocyclic structures with the goal of stimulating further progress in this field. The superiorities of this procedure are high yield of product, low amounts of catalyst and short reaction time.

Al-Humaidi J, Zaki MEA, Fathalla M, Gomha SM. Mechanochemical Synthesis and Molecular Docking Studies of New Azines Bearing Indole as Anticancer Agents

The development of new approaches for the synthesis of new bioactive heterocyclic derivatives is of the utmost importance for pharmaceutical industry. In this regard, the present study reports the green synthesis of new benzaldazine and ketazine derivatives via the condensation of various carbonyl compounds (aldehydes and ketones with the 3-(1-hydrazineylideneethyl)-1H-indole using the grinding method with one drop of acetic acid). Various spectroscopic techniques were used to identify the structures of the synthesized derivatives. Furthermore, the anticancer activities of the reported azine derivatives were evaluated against colon, hepatocellular, and breast carcinoma cell lines using the MTT technique with doxorubicin as a reference medication. The findings suggested that the synthesized derivatives exhibited potential anti-tumor activities toward different cell lines. For example, 3c, 3d, 3h, 9, and 13 exhibited interesting activity with an IC50 value of 4.27-8.15 µM towards the HCT-116 cell line as compared to doxorubicin (IC50 = 5.23 ± 0.29 µM). In addition, 3c, 3d, 3h, 9, 11, and 13 showed excellent cytotoxic activities (IC50 = 4.09-9.05 µM) towards the HePG-2 cell line compared to doxorubicin (IC50 = 4.50 ± 0.20 µM), and 3d, 3h, 9, and 13 demonstrated high potency (IC50 = 6.19-8.39 µM) towards the breast cell line (MCF-7) as compared to the reference drug (IC50 = 4.17 ± 0.20 µM). The molecular interactions between derivatives 3a-h, 7, 9, 11, 13, and the CDK-5 enzyme (PDB ID: 3IG7) were studied further using molecular docking indicating a high level of support for the experimental results. Furthermore, the drug-likeness analysis of the reported derivatives indicated that derivative 9 (binding affinity = -8.34 kcal/mol) would have a better pharmacokinetics, drug-likeness, and oral bioavailability as compared to doxorubicin (-7.04 kcal/mol). These results along with the structure-activity relationship (SAR) of the reported derivatives will pave the way for the design of additional azines bearing indole with potential anticancer activities.

Bioprospecting phytochemicals of Rosmarinus officinalis L. for targeting SARS-CoV-2 main protease (Mpro): a computational study

CONTEXT

The persistent spread of highly contagious COVID-19 disease is one of the deadliest occurrences in the history of mankind. Despite the distribution of numerous efficacious vaccines and their extensive usage, the perpetual effectiveness of immunization is being catechized. Therefore, discovering an alternative therapy to control and prevent COVID-19 infections has become a top priority. The main protease (M^pro) plays a key role in viral replication, making it an intriguing pharmacological target for SARS-CoV-2.

METHODS

In this context, virtual screening of thirteen bioactive polyphenols and terpenoids of Rosmarinus officinalis L. was performed using several computational modules including molecular docking, ADMET, drug-likeness characteristics, and molecular dynamic simulation to predict the potential inhibitors against SARS-CoV-2 M^pro (PDB: 6LU7). The results suggest that apigenin, betulinic acid, luteolin, carnosol, and rosmarinic acid may emerge as potential inhibitors of SARS-CoV-2 with acceptable drug-likeness, pharmacokinetics, ADMET characteristics, and binding interactions comparable with remdesivir and favipiravir. These findings imply that some of the active components of Rosmarinus officinalis L. can serve as an effective antiviral source for the development of therapeutics for SARS-CoV-2 infection.

A Novel Ambroxol-Derived Tetrahydroquinazoline with a Potency against SARS-CoV-2 Proteins

We report synthesis of a novel 1,2,3,4-tetrahydroquinazoline derivative, named 2-(6,8-dibromo-3-(4-hydroxycyclohexyl)-1,2,3,4-tetrahydroquinazolin-2-yl)phenol (1), which was obtained from the hydrochloride of 4-((2-amino-3,5-dibromobenzyl)amino)cyclohexan-1-ol (ambroxol hydrochloride) and salicylaldehyde in EtOH. The resulting compound was produced in the form of colorless crystals of the composition 1∙0.5EtOH. The formation of the single product was confirmed by the IR and 1H spectroscopy, single-crystal and powder X-ray diffraction, and elemental analysis. The molecule of 1 contains a chiral tertiary carbon of the 1,2,3,4-tetrahydropyrimidine fragment and the crystal structure of 1∙0.5EtOH is a racemate. Optical properties of 1∙0.5EtOH were revealed by UV-vis spectroscopy in MeOH and it was established that the compound absorbs exclusively in the UV region up to about 350 nm. 1∙0.5EtOH in MeOH exhibits dual emission and the emission spectra contains bands at about 340 and 446 nm upon excitation at 300 and 360 nm, respectively. The DFT calculations were performed to verify the structure as well as electronic and optical properties of 1. ADMET properties of the R-isomer of 1 were evaluated using the SwissADME, BOILED-Egg, and ProTox-II tools. As evidenced from the blue dot position in the BOILED-Egg plot, both human blood-brain barrier penetration and gastrointestinal absorption properties are positive with the positive PGP effect on the molecule. Molecular docking was applied to examine the influence of the structures of both R-isomer and S-isomer of 1 on a series of the SARS-CoV-2 proteins. According to the docking analysis results, both isomers of 1 were found to be active against all the applied SARS-CoV-2 proteins with the best binding affinities with Papain-like protease (PLpro) and nonstructural protein 3 (Nsp3_range 207-379-AMP). Ligand efficiency scores for both isomers of 1 inside the binding sites of the applied proteins were also revealed and compared with the initial ligands. Molecular dynamics simulations were also applied to evaluate the stability of complexes of both isomers with Papain-like protease (PLpro) and nonstructural protein 3 (Nsp3_range 207-379-AMP). The complex of the S-isomer with Papain-like protease (PLpro) was found to be highly unstable, while the other complexes are stable.

Copper(II) Chelates of Schiff Bases Enriched with Aliphatic Fragments: Synthesis, Crystal Structure, In Silico Studies of ADMET Properties and a Potency against a Series of SARS-CoV-2 Proteins

We report two complexes [Cu(LI)2] (1) and [Cu(LII)2] (2) (HLI = N-cyclohexyl-3-methoxysalicylideneimine, HLII = N-cyclohexyl-3-ethoxysalicylideneimine). The ligands in both complexes are trans-1,5-N,O-coordinated, yielding a square planar CuN2O2 coordination core. The molecule of 1 is planar with two cyclohexyl groups oriented to the opposite sites of the planar part of a molecule, while the molecule of 2 is significantly bent with two cyclohexyl groups oriented to the same convex site of a molecule. It was established that both complexes in MeOH absorb in the UV region due to intraligand transitions and LMCT. Furthermore, the UV-vis spectra of both complexes revealed two low intense shoulders in the visible region at about 460 and 520 nm, which were attributed to d-d transitions. Both complexes were predicted to belong to a fourth class of toxicity with the negative BBB property and positive gastrointestinal absorption property. According to the molecular docking analysis results, both complexes are active against all the applied SARS-CoV-2 proteins with the best binding affinity with Nsp 14 (N7-MTase), PLpro and Mpro. The obtained docking scores of complexes are either comparable to or even higher than those of the initial ligands. Complex 1 was found to be more efficient upon interaction with the applied proteins in comparison to complex 2. Ligand efficiency scores for the initial ligands, 1 and 2 were also revealed.

Recent Development of Small Molecules for SARS-CoV-2 and the Opportunity for Fragment-Based Drug Discovery

Abstract:

The ongoing pandemic of Covid-19 caused by SARS-CoV-2 is a major threat to global public health, drawing attention to develop new therapeutics for treatment. Much research work is focused on identifying or repurposing new small molecules to serve as potential inhibitors by interacting with viral or host-cell molecular targets and understanding the nature of the virus in the host cells. Identifying small molecules as potent inhibitors at an early stage is advantageous to make a molecule with higher potency and then find a lead compound for the development of drug discovery. Small molecules can show their inhibition property by targeting either SARS-CoV-2 main protease (Mpro) enzyme, papain-like protease (PLpro) enzyme, or helicase (Hel), or blocking the spike (S) protein angiotensin-converting enzyme 2 (ACE2) receptor. A very recent outbreak of a new variant (B.1.617.2—termed as Delta variant) of SARS-CoV-2 worldwide posed a greater challenge as it is resistant to clinically undergoing vaccine trials. Thus, the development of new drug molecules is of potential interest to combat SARS-CoV-2 disease, and for that, fragment-based drug discovery (FBDD) approach could be one of the ways to bring out an effective solution. Two cysteine protease enzymes would be an attractive choice of target for fragment-based drug discovery to tune the molecular structure at an early stage with suitable functionality. In this short review, the recent development of small-molecule as inhibitors against Covid-19 are discussed and the opportunity for FBDD is envisioned optimistically to provide an outlook regarding Covid-19 that may pave the way in the direction of the Covid-19 drug development paradigm.

Structure-based design and synthesis of copper(ii) complexes as antivirus drug candidates targeting SARS CoV-2 and HIV

This paper describes the structure-based design and synthesis of two novel square-planar trans-N2O2 Cu(ii) complexes [Cu(L1)2] (1) and [Cu(L2)2] (2) of 2-((Z)-(4-methoxyphenylimino)methyl)-4,6-dichlorophenol (L1H) and 2-((Z)-(2,4-dibromophenylimino)methyl)-4-bromophenol (L2H) as potential inhibitors against the main protease of the SARS-CoV-2 and HIV viruses.

Synthesis and characterization of novel copper(ii) complexes as potential drug candidates against SARS-CoV-2 main protease

Two novel copper(ii) Schiff base complexes, [Cu(L1)2] (1) and [Cu(L2)(CH3OH)(Cl)] (2) of [(Z)-(5-chloro-2-((3,5-dichloro-2-hydroxybenzylidene)amino)phenyl)(phenyl)methanone (L1H) and (Z)-(2((5-bromo-2-hydroxybenzylidene)amino-5-chlorophenyl)(phenyl)methanone)(L2H)], have been designed, synthesized and characterized.

In-silico design and ADMET predictions of some new imidazo[1,2-a]pyridine-3-carboxamides (IPAs) as anti-tubercular agents

Tuberculosis (TB) is one of the leading infectious diseases worldwide even with the ravaging COVID-19 pandemic in recent times. This mandated further search and exploration of more possible anti-TB drug candidates against M. tuberculosis strains. As an extension of our previous work on the homology modeled cytochrome b subunit of the bc1 complex (QcrB) of Mycobacterium tuberculosis, an in-silico design was carried out in order to further explore more newly potential anti-TB compounds. Ligand 26 was selected as the lead template (scaffold A) based on our previous docking results and its less bulky structure. Successively, eight (8) new ligands (A1–A8) were designed with better binding affinities in comparison to the scaffold template (−6.8 kcal/mol) and isoniazid standard drug (−6.00 kcal/mol) respectively. In addition, three (3) designed ligands namely, A6, A2, and A7 with higher binding affinities were validated via ADME and toxicity prediction analysis, and the results showed zero violations of Lipinski rules with similar bioavailability, and high rate in gastrointestinal absorption, while toxicity parameters such as carcinogenicity and cytotoxicity were all predicted as non-toxic (inactiveness). The designed IPA compounds in the present study could serve as a promising gateway that could help the medicinal and synthetic chemist in the exploration of a new set of derivatives as anti-TB agents. Therefore, this research strongly recommends further experimental consideration of the newly designed IPA compounds through synthesis, in-vitro and in-vivo studies to validate the theoretical findings.

In Silico Investigation of Phytoconstituents of Medicinal Herb 'Piper Longum' Against SARS-CoV-2 by Molecular Docking and Molecular Dynamics Analysis

Unavailability of treatment for the SARS-CoV-2 virus has raised concern among the population worldwide. This has led to many attempts to find alternative options to prevent the infection of the disease, including focusing on vaccines and drugs. The use of natural products and herbal extracts can be a better option in beating the virus and boosting up immunity. In the present paper, we have done a systematic in silico study of papain-like protease of COVID-19 virus with the chemical constituents of herbal plant Piper Longum. Screening of the pharmacokinetic properties is done with thirty-two phytoconstituents of Piper Longum which help us in selecting the most active components of the plant. After selection molecular docking is performed with Aristololactam (C17H11NO4), Fargesin (C21H22O6), l-asarinin (C20H18O6), Lignans Machilin F (C20H22O5), Piperundecalidine (C23H29NO3), and Pluviatilol (C20H20O6). Molecular dynamic (MD) is also performed with the inhibitor-receptor complex which suggest significant inhibition and a stable complex of I-Asarinin with PLpro. Docking scores and simulation results suggest that I-Asarinin can act as a potential drug like candidate against COVID-19.