Silico Docking Studies Research Articles

Targeting Oral Cancer: In Silico Docking Studies of Phytochemicals on Oncogenic Molecular Markers.

Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. Oral carcinogenesis is a complex, multistep process in which genetic events within signal transduction pathways governing normal cellular physiology are quantitatively or qualitatively altered. There are various molecular targets like Cyclin D and PI3k- alpha Ras Binding Domain receptor protein involved in the pathogenesis of Oral Squamous Cell Carcinoma. The aim of the study is to demonstrate the computer aided drug design to identify a potent natural molecule for targeting cyclin D4 and PI3K RAS binding protein. Target selection (Cyclin D1 and PI3K-alpha Ras Binding Domain receptor) was done and structures were derived from protein data bank. Ligands (Apigenin, Chrysoeriol and Luteolin) selection was done and structure derived. Final docking was performed by Autodock. From the docking results it can be seen that luteolin has the highest binding energy (-5.45) with the Cyclin D receptor molecule followed by Chrysoeriol (-4.99) and Apigenin (-4.96). The binding energies of the ligands against PI3K-alpha Ras Binding Domain receptors were Apigenin (-4.51), Chrysoeriol (-4.6) and Luteolin (-4.56). The study concludes that all the three selected ligands possess high binding energy with both the target proteins involved in carcinogenesis with highest binding energy possessed by Luteolin against the Cyclin D receptor and by Chrysoeriol against PI3K-RAS binding protein. Thus their activity can be utilized to derive potential Anti-cancer therapeutic drugs.

6-Amino-4-aryl-7-phenyl-3-(phenylimino)-4,7-dihydro-3H-[1,2]dithiolo[3,4-b]pyridine-5-carboxamides: Synthesis, Biological Activity, Quantum Chemical Studies and In Silico Docking Studies.

New [1,2]dithiolo[3,4-b]pyridine-5-carboxamides were synthesized through the reaction of dithiomalondianilide (N,N'-diphenyldithiomalondiamide) with 3-aryl-2-cyanoacrylamides or via a three-component reaction involving aromatic aldehydes, cyanoacetamide and dithiomalondianilide in the presence of morpholine. The structure of 6-amino-4-(2,4-dichloro- phenyl)-7-phenyl-3-(phenylimino)-4,7-dihydro-3H-[1,2]dithiolo[3,4-b]pyridine-5-carboxamide was confirmed using X-ray crystallography. To understand the reaction mechanism in detail, density functional theory (DFT) calculations were performed with a Grimme B97-3c composite computational scheme. The results revealed that the rate-limiting step is a cyclization process leading to the closure of the 1,4-dihydropyridine ring, with an activation barrier of 28.8 kcal/mol. Some of the dithiolo[3,4-b]pyridines exhibited moderate herbicide safening effects against 2,4-D. Additionally, ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) parameters were calculated and molecular docking studies were performed to identify potential protein targets.

In Silico Docking Studies of Potential Phytocompounds from Musa Flowers against Endometritis

In Silico Docking Studies of Potential Phytocompounds from Musa Flowers against Endometritis

In Silico Activity Prediction and Docking Studies of the Binding Mechanisms of Levofloxacin Structure Derivatives to Active Receptor Sites of Bacterial Type IIA Topoisomerases

The need for new antimicrobial agents (AntAg) is driven by the persistent antibiotic resistance in microorganisms, as well as the increasing frequency of pandemics. Due to the deficiency of AntAg, research aimed at developing speedy approaches to find new drug candidates is relevant. This study aims to conduct an in silico study of the biological activity spectrum as well as the molecular binding mechanisms of four structurally different forms of levofloxacin (Lvf) with bacterial topoisomerases targets of type IIA (DNA gyrase and topoisomerase IV) to enable the development of drugs with an improved characterization of the safety profile. To achieve this goal, a number of software products were used, such as ChemicPen v. 2.6, PyMol 2.5, Avogadro 1.2.0, PASS, AutoDockTools 1.5.7 with the new generation software Autodock Vina. These software products are the first to be made available for visualization of clusters with determination of ligand-receptor pair binding affinity, as well as clustering coordinates and proposed mechanisms of action. One of the real structures of Lvf, a decarboxylated derivative, was obtained with tribochemical (TrbCh) exposure. The action spectrum of molecular ligands is described based on a Bayesian probability activity prediction model (PASS software Version 2.0). Predicted and real (PMS and RMS) molecular structures of Lvf, with decreasing levels of structural complexity, were translated into descriptors via Wiener (W), Balaban (Vs), Detour (Ip), and Electropy € indices. The 2D «structure-activity» diagrams were used to differentiate closely related structures of levofloxacin. PMS and RMS were visualized as 3D models of the ligand-receptor complexes. The contact regions of RMS and PMS with key amino acid residues—SER-79, DT-15, DG-1, DA-1—were demonstrated. The intra- and inter-molecular binding sites, data on free energy (affinity values, kcal/mol), the binding constant Kb (M−1), and the number of clusters are presented. The research results obtained from the presented in silico approach to explore the spectrum of action find quantitative “structure-activity” correlations, and predict molecular mechanisms may be of applied interest for directed drug discovery.

Efficient Synthesis of Natural Product Inspired Naphthoquinone-Fused Glycohybrids and Their In Silico Docking Studies

AbstractNaphthoquinones, a diverse group of natural compounds with a 1,4-naphthoquinone core structure, have gained attention for their pharmacological properties. The anticancer activity of these compounds is attributed to their ability to accept electrons, leading to the generation of reactive oxygen species that cause DNA damage and cell death. In recent studies, hydroxy-1,4-naphthoquinone derivatives, including daunorubicin, have shown promising inhibitory effects against several human cancers, such as acute myeloid leukemia, chronic myelogenous leukemia, and Kaposi’s sarcoma. To further explore their potential as anticancer agents, this research article focuses on the design and synthesis of natural product inspired naphthoquinone-based glycohybrids. These glycohybrids are designed based on the structures of bioactive aryl glycosides and quinones, aiming to enhance their binding affinity and specificity towards cancer-related protein targets. The interactions between the synthesized glycohybrids and target proteins through computational docking simulations has been studied and better binding affinity was found.

In Silico Docking Studies, Synthesis, Characterization, and Antimicrobial Antimycobacterial Activity of Coumarinyl Oxadiazoles from Fatty Acids

In Silico Docking Studies, Synthesis, Characterization, and Antimicrobial Antimycobacterial Activity of Coumarinyl Oxadiazoles from Fatty Acids

3-Ferrocenyl-estra-1,3,5 (10)-triene-17-one: Synthesis, Crystal Structure, Hirshfeld Surface Analysis, DFT Studies, and Its Binding to Human Serum Albumin Studied through Fluorescence Quenching and In Silico Docking Studies.

3-ferrocenyl-estra-1,3,5 (10)-triene-17-one (2), [Fe(C5H5)(C24H25O3)], crystallizes in the monoclinic space group C2. The cyclopentadienyl (Cp) rings adopt a nearly eclipsed conformation, and the Cp plane is tilted by 87.66° with respect to the substituted phenyl plane. An average Fe-C(Cp) bond length of 2.040(13) Å was determined, similar to the one reported for ferrocene. Hirshfeld surfaces and two-dimensional fingerprint plots were generated to analyze weak intermolecular C-H···π and C-H···O interactions. Density functional theory studies revealed a 1.15 kcal/mol rotational barrier for the C3-O1 single bound. Fluorescence quenching studies and in silico docking studies suggest that human serum albumin forms a complex with 2 via a static mechanism dominated by van der Waals interactions and hydrogen bonding interactions.

In Silico Analysis and Docking Studies on Cystic Fibrosis to identify Potential Drug Candidates

Cystic fibrosis (CF) is a multi-system autosomal recessive disorder due to defects in the CF transmembrane conductance regulator (CFTR) protein, most commonly affecting the lungs. Despite being thought of as an uncommon ailment, cystic fibrosis (CF) is the most common monogenic sickness among those who are mostly of European descent. It is estimated that 1% of people worldwide have a single faulty copy of the CFTR gene. A recent pilot study using NGS technology in 2020 from Delhi’s Sir Ganga Ram Hospital, indicated the prevalence of cystic fibrosis mutations of 1 in 2,000 persons. This is much higher than the earlier estimated prevalence as the disease was rare in the Indian population. The most common mutations are delta F 508 and G551D which are also prevalent in the Indian population. The use of computer-aided drug design (CADD) can reduce the time needed for the discovery, evaluation and structure-optimization of new therapeutic candidates. CADD may be advantageous for pharmaceuticals with logical designs. Multiple breakthroughs have been made in the study of small molecule medicines and natural chemicals for the treatment of cystic fibrosis. Seven well-known small-molecule medications that target the CFTR were chosen including Ivacaftor, Lumacaftor, Tezacaftor, Galicaftor, Olacaftor, Navocaftor and Elexacaftor. The natural compounds chosen were Genistein, Curcumin and Resveratrol. They were all docked onto the CFTR target protein and the effectiveness of the therapy was evaluated based on the docking scores. It was also planned to investigate if the combined impacts of these two different kinds of molecules may help in the development of new medications. To achieve this, combinatorial docking was tried using the small molecule market medication and the natural chemical that showed the best interaction with the target protein. Finally, based on molecular docking studies, Lonidamine, a well-known medicinal molecule was used to determine whether it may target cystic fibrosis.

Novel Oleanolic Acid-Phtalimidines Tethered 1,2,3 Triazole Hybrids as Promising Antibacterial Agents: Design, Synthesis, In Vitro Experiments and In Silico Docking Studies.

As part of the valorization of agricultural waste into bioactive compounds, a series of structurally novel oleanolic acid ((3β-hydroxyolean-12-en-28-oic acid, OA-1)-phtalimidines (isoindolinones) conjugates 18a-u bearing 1,2,3-triazole moieties were designed and synthesized by treating an azide 4 previously prepared from OA-1 isolated from olive pomace (Olea europaea L.) with a wide range of propargylated phtalimidines using the Cu(I)-catalyzed click chemistry approach. OA-1 and its newly prepared analogues, 18a-u, were screened in vitro for their antibacterial activity against two Gram-positive bacteria, Staphylococcus aureus and Listeria monocytogenes, and two Gram-negative bacteria, Salmonella thyphimurium and Pseudomonas aeruginosa. Attractive results were obtained, notably against L. monocytogenes. Compounds 18d, 18g, and 18h exhibited the highest antibacterial activity when compared with OA-1 and other compounds in the series against tested pathogenic bacterial strains. A molecular docking study was performed to explore the binding mode of the most active derivatives into the active site of the ABC substrate-binding protein Lmo0181 from L. monocytogenes. Results showed the importance of both hydrogen bonding and hydrophobic interactions with the target protein and are in favor of the experimental data.

Synthesis, Physicochemical Characterization, Biological Evaluation, In Silico and Molecular Docking Studies of Pd(II) Complexes with P, S-Donor Ligands.

One homoleptic (1) and three heteroleptic (2-4) palladium(II) complexes were synthesized and characterized by various physicochemical techniques, i.e., elemental analysis, FTIR, Raman spectroscopy, 1H, 13C, and 31P NMR. Compound 1 was also confirmed by single crystal XRD, showing a slightly distorted square planar geometry. The antibacterial results obtained via the agar-well diffusion method for compound 1 were maximum among the screen compounds. All the compounds have shown good to significant antibacterial results against the tested bacterial strains, Escherichia coli, Klebsiella pneumonia, and Staphylococcus aureus, except 2 against Klebsiella pneumonia. Similarly, the molecular docking study of compound 3 has shown the best affinity with binding energy scores of -8.6569, -6.5716, and -7.6966 kcal/mol against Escherichia coli, Klebsiella pneumonia, and Staphylococcus aureus, respectively. Compound 2 has exhibited the highest activity (3.67 µM), followed by compound 3 (4.57 µM), 1 (6.94 µM), and 4 (21.7 µM) against the DU145 human prostate cancer cell line using the sulforhodamine B (SRB) method as compared to cisplatin (>200 µM). The highest docking score was obtained for compounds 2 (-7.5148 kcal/mol) and 3 (-7.0343 kcal/mol). Compound 2 shows that the Cl atom of the compound acts as a chain side acceptor for the DR5 receptor residue Asp B218 and the pyridine ring is involved in interaction with the Tyr A50 residue via arene-H, while Compound 3 interacts with the Asp B218 residue via the Cl atom. The physicochemical parameters determined by the SwissADME webserver revealed that no blood-brain barrier (BBB) permeation is predicted for all four compounds, while gastrointestinal absorption is low for compound 1 and high for the rest of the compounds (2-4). As concluding remarks based on the obtained in vitro biological results, the evaluated compounds after in vivo studies might be a good choice for future antibiotics and anticancer agents.

In Silico docking studies on thrombolytic properties ofHomoeopathic Medicine Cactus grandiflorus by activationof tissue-Plasminogen Activator in the treatment of Vascular Thrombosis

In Silico docking studies on thrombolytic properties ofHomoeopathic Medicine Cactus grandiflorus by activationof tissue-Plasminogen Activator in the treatment of Vascular Thrombosis

In Silico docking studies on thrombolytic properties ofHomoeopathic Medicine Cactus grandiflorus by activationof tissue-Plasminogen Activator in the treatment of Vascular Thrombosis

In Silico docking studies on thrombolytic properties ofHomoeopathic Medicine Cactus grandiflorus by activationof tissue-Plasminogen Activator in the treatment of Vascular Thrombosis

Screening of Spirulina Components for Anti-Parkinson's and Anti-Alzheimer's Activity byin Silico Methods and Docking Studies.

Spirulina platensis was first isolated from Lake Texcoco by Aztecs in the sixteenth century. In 2012, spirulina was considered to be safe dietary supplement by the Food and Drug Administration (FDA). Spirulina is a cyanophytic microalgae that is often considered as single cell protein. It contains many essential amino acids, proteins, fatty acids, antioxidant pigments, carotenoids, and cyanogenic pigments, that is, phycocyanobilins and phycocyanins (Eriksen, Appl Microbiol Biotechnol, 80(1):1-4, 2008). Components of spirulina are investigated for many health benefits and for pharmaceutical uses (Karkos et al., Spirulina in clinical practice: evidence-based human applications). Spirulina has been found to have a role in growth, immunity (Wu et al., Arch Toxicol, 90(8):1817-40, 2016), antioxidant (Wu et al., Arch Toxicol, 90(8):1817-40, 2016), antiviral (Ayehunie et al., J Acquir Immune Defic Syndr Hum Retrovirol, 18(1):7-12, 1998), antitoxicologic, anti-cancerogenic (Hirahashi et al., Int Immunopharmacol, 2(4):423-34, 2002), antidiabetic (Layam and Reddy, Diabetol Croat, 35(2):29-33, 2006), and neuroprotective properties. In this study, we focused on spirulina components in anti-Parkinson's and anti-Alzheimer's activity. Four potential targets, two for each activity, that is, structure of parkinE3 ligase (PDB ID:4I1H) and structure of BACE bound to 5-(3-(5-chloropyridin-3-yl)phenyl)-5-cyclopropyl-2-imino-3-methylimidazolidin-4one (PDBI D:4DJx) for anti-Parkinson's activity and structure of human MAO B in complex with selective inhibitor safinamide (PDB ID:2V5Z) and crystal structure of human BACE-1 in complex with CNP520(PDB ID:6EQM) for anti-Alzheimer's activity, have been selected. The in silico results and scoring of virtual screening, that is, molecular docking, were compared with commonly used marketed drugs such as levodopa for Parkinson's disease (PD) and rivastigmine (Rösler et al., BMJ, 318(7184):633-40, 1999) for Alzheimer's disease.

Bioprospecting of Phytoconstituents from Tamarind Pulp and In Silico Docking Studies of Flavonol Against Uropathogenic Bacterial Proteins

Bioprospecting of Phytoconstituents from Tamarind Pulp and In Silico Docking Studies of Flavonol Against Uropathogenic Bacterial Proteins

Methyldecanoate isolated from marine algae Turbinaria ornata enhances immunomodulation in LPS-induced inflammatory reactions in RAW 264.7 macrophages via iNOS/NFκB pathway.

This study identifies the anti-inflammatory, antioxidant, and immunomodulatory potential of a fatty acid methyl ester segregated from the brown algaeTurbinaria ornataand identified by nuclear magnetic resonance and mass spectrometry as methyl 6,12-dimethyltridecanoate (ET). Antioxidant and anti-inflammatory effectsof ET were studied on lipopolysaccharide (LPS)-induced inflammatory reaction in RAW 264.7 macrophages. Moreover,in silicodocking studies of isolated ET with inflammatory markers TNFα, NFκB, and COX-2 showed potent binding scores suggesting anti-inflammatory potential. ET significantly reduced LPO and increased LPS-induced SOD, catalase, and GSH levels. Molecular docking results were further confirmed by checking mRNA levels of selected cytokines (IL6 and IL10), followed by protein expression of iNOS and NFκB in LPS-induced macrophages. ET significantly upregulated the expression of IL10 and downregulated the expression of IL6, iNOS, and NFκB, confirming the inhibition of LPS-induced inflammation via the iNOS/NFκB pathway.

Identification of potential candidate vaccines against Mycobacterium ulcerans based on the major facilitator superfamily transporter protein.

Buruli ulcer is a neglected tropical disease that is characterized by non-fatal lesion development. The causative agent is Mycobacterium ulcerans (M. ulcerans). There are no known vectors or transmission methods, preventing the development of control methods. There are effective diagnostic techniques and treatment routines; however, several socioeconomic factors may limit patients' abilities to receive these treatments. The Bacillus Calmette-Guérin vaccine developed against tuberculosis has shown limited efficacy, and no conventionally designed vaccines have passed clinical trials. This study aimed to generate a multi-epitope vaccine against M. ulcerans from the major facilitator superfamily transporter protein using an immunoinformatics approach. Twelve M. ulcerans genome assemblies were analyzed, resulting in the identification of 11 CD8+ and 7 CD4+ T-cell epitopes and 2 B-cell epitopes. These conserved epitopes were computationally predicted to be antigenic, immunogenic, non-allergenic, and non-toxic. The CD4+ T-cell epitopes were capable of inducing interferon-gamma and interleukin-4. They successfully bound to their respective human leukocyte antigens alleles in in silico docking studies. The expected global population coverage of the T-cell epitopes and their restricted human leukocyte antigens alleles was 99.90%. The population coverage of endemic regions ranged from 99.99% (Papua New Guinea) to 21.81% (Liberia). Two vaccine constructs were generated using the Toll-like receptors 2 and 4 agonists, LprG and RpfE, respectively. Both constructs were antigenic, non-allergenic, non-toxic, thermostable, basic, and hydrophilic. The DNA sequences of the vaccine constructs underwent optimization and were successfully in-silico cloned with the pET-28a(+) plasmid. The vaccine constructs were successfully docked to their respective toll-like receptors. Molecular dynamics simulations were carried out to analyze the binding interactions within the complex. The generated binding energies indicate the stability of both complexes. The constructs generated in this study display severable favorable properties, with construct one displaying a greater range of favorable properties. However, further analysis and laboratory validation are required.

Antihypertensive and In Silico Docking Studies OF Phytoconstituents Isolated from Syzygium Alternifolium Bark

Aim of the Study: Pharmacological examination was done for methanolic extract Syzygium alternifolium bark (MESA) for its antihypertensive activity, Angiotensin converting enzyme (ACE) inhibition by in vitro and in vivo studies, antioxidant activity via radical scavenging activity.
 Methods: Albino Wistar rats were allowed to treat with dexamethasone (30 μg/kg/day s.c) or saline for about 14 days. Methanolic extract of Syzygium alternifolium (300 mg/kg, b.w., p.o.) is administered from day 8 to 14 day of study to the treatment group. Chronic fructose treatment in rats showed to increase blood pressure in relationship with insulin blockade. MESA (300 mg/kg b.w, p.o) was capable of preventing the origin of hypertension by diminishing the raised blood levels i.e., blood pressure.
 Results and Discussion: The decrease in the blood pressure is accredited to the restraint of ACE. The preliminary phytochemical examination suggests that the MESA has alkaloids, flavonoids, glycosides, steroids, sugars, proteins and tannins. MESA exhibited 1, 1-diphenyl-2-picrylhydrazyl interrupting radical chain reactions with IC50 value of 12.34 µg/ml just as superoxide radical scavenging ability with IC50 value of 21 µg/ml. MESA showed antihypertensive activity by limiting angiotensin converting enzyme and interrupted free radical reactions i.e., antioxidant property. These findings reveal the existence of probable active constituents of MESA. Understanding the molecular method of activity of natural product is a vital stage for creating drugs from them. The docking studies of the number of compounds were performed using mCule software. The constituents have good binding ability with ACE 1 inhibitor, Calcium channel blocker, and Renin inhibitor proteins and Ramachandran plot is analyzed.
 Conclusion: The compounds from Syzygium alternifolium bark have shown antihypertensive activity when compared with standard drug Amlodipine.

Ecdysteroids as Potent Enzyme Inhibitors and Verification of Their Activity Using In Vitro and In Silico Docking Studies.

Ecdysteroids represent arthropods’ steroidal hormones, and they exist in about 5–6% of plant species. In this study, the enzyme inhibitory activity of 20 ecdysteroids was assessed for the first time via determining their inhibition versus acetylcholinesterase, butyrylcholinesterase, tyrosinase, as well as α-amylase enzymes. Furthermore, 20-Hydroxyecdysone-2,3,22-tri-O-acetate (4) showed the highest inhibition of acetylcholinesterase and butyrylcholinesterase with values of 5.56 and 4.76 mg GALAE/g, respectively. All ecdysteroids displayed tyrosinase inhibitory effects, whereas the most potent was viticosterone E (7) with 78.88 mg KAE/g. Most ecdysteroids had similar amylase inhibitory properties; meanwhile, the best α-amylase inhibitory potential was observed with viticosterone E-diacetonide (18) (0.35 mmol ACAE/g). Most of the tested compounds showed tyrosinase inhibitory potential; therefore, they were exposed to molecular docking evaluation using the tyrosinase enzyme. Viticosterone E (7) showed the best ranking score with a docking score of −5.716 Kcal/mol and made three separate H-bonds with Gly281, Asn81, and His85. From ADMET /TOPKAT in silico evaluation, it was obvious that most of the compounds displayed reasonable pharmacodynamic and pharmacokinetic properties; however, their toxicity should be carefully monitored by adjusting their doses while investigating their activity after incorporation into dosage forms. Principal component analysis (PCA) based upon the in vitro and in silico data was carried out to visualize the differences between the tested compounds better. PCA score plot successfully classifies the compounds into four main clusters that, in turn, reflects the similarities and differences among the clustered compounds with respect to their biological, pharmacokinetic, and pharmacodynamic properties that are mainly influenced by the similarity in the chemical structure. Thus, ecdysteroids can act as effective drug entities for alleviating several disorders owing to their enzyme inhibitory potential.

Cholinesterase Inhibitory Activities and In Silico Docking Studies of Blumeatin Isolated from Blumea balsamifera L. DC.

Cholinesterase inhibition provides symptomatic treatment for neurodegenerative diseases such as Alzheimer’s disease. Commercially available drugs on the market mostly target acetylcholinesterase. However, evidence suggests that selective inhibition of butyrylcholinesterase may lead to greater efficacy with fewer side effects and slower disease progression. The aim of this research was to isolate a butyrylcholinesterase-selective inhibitor from Blumea balsamifera L. DC. In vitro cholinesterase assays were used to evaluate the inhibitory activity and mechanism of action of blumeatin. Molecular docking studies were performed to support the BuChE- selectivity of blumeatin. Blumeatin inhibited BuChE in a concentration-dependent manner, with an IC50 of 136.3 ± 12.6 μM and a selectivity ratio of 1.395 for BuChE over AChE. Additionally, the Ki of blumeatin is 10 times lower in BuChE compared to AChE. Molecular docking studies confirmed the selectivity, as revealed by the tighter hydrogen bonding of blumeatin with the BuChE’s active site. Blumeatin acts as a competitive inhibitor and a noncompetitive inhibitor of BuChE and AChE, respectively. With these results, blumeatin could be a potential lead as a drug treatment for AD because of its butyrylcholinesterase selectivity.

Coordination Versatility of Metal Complexes in the Presence of Heterocyclic Bases as Auxiliary Ligands: Synthesis, Spectroscopic Studies, Structural Characterization, Antibacterial Activity and in Silico Docking Studies

Coordination Versatility of Metal Complexes in the Presence of Heterocyclic Bases as Auxiliary Ligands: Synthesis, Spectroscopic Studies, Structural Characterization, Antibacterial Activity and in Silico Docking Studies