Evaluation of electronic, lipophilic and membrane affinity effects on antiproliferative activity of 5-substituted-2-(2,4-dihydroxyphenyl)-1,3,4-thiadiazoles against various human cancer cells

Inhibitors against New Delhi metallo-betalactamase-1 (NDM-1) and its variants endemic in Indian settings along with the laboratory functional gain mutant of NDM-1

PURPOSE

The emergence of NDM-1 producing bacteria has become common in both hospital and community settings, but no inhibitor has yet been available for clinical treatment. Hence, demanding the urgent need of NDM-1 inhibitors, we initiated to screen broad spectrum inhibitors against NDM natural variants and laboratory mutant.

METHODS

We used docking and molecular dynamics simulations, in silico pharmacokinetic investigations, and density functional theory calculation to characterize molecules. Furthermore, an in vitro study, including MIC, kinetics, and fluorescence study were carried out to confirm the efficacies of the selected compounds.

RESULTS

According to the findings of the computational studies, three compounds were effective against NDM variants. Fourfold reduction in MIC of imipenem and meropenem was observed when combined with inhibitors (D2573, D2148, and D63) against blaNDM-1, blaNDM-4, blaNDM-6, and blaNDM-1Q123A, while twofold reduction in MIC of imipenem and meropenem was observed against blaNDM-5 and blaNDM-7. Similarly in the presence of inhibitors (D2573, D2148, and D63) the efficiency of nitrocefin hydrolysis by NDM-4, NDM-6, and Q123A decreases to much more extent as compared to NDM-5 and NDM-7. These results showed that the efficacy of these broad spectrum inhibitors decreases with increasing resistance of NDM variants.

CONCLUSION

This is the first time inhibitors were tested against different NDM natural variants which are endemic in Indian settings. Moreover, a functional gain laboratory mutant was also checked for their efficacies. We may propose these molecules for the pre-clinical trial to further translate.

Repurposing FDA approved drug molecules against A B C classes of β-lactamases: a computational biology and molecular dynamics simulations study

β-lactamase are the main resistance factor for β-lactam antibiotics in Gram-negative bacteria. Since β-lactam antibiotics are being utilised as an antimicrobial agents extensively for the past 70 years, a large number of β-lactam-inactivating β-lactamases have been produced by bacteria. Here, we employed a structure-based drug discovery approach to identify and assess the efficacy of a potential medication that might block the β-lactamases which hydrolyse antibiotics. The FDA-approved medications were subjected to virtual screening, molecular docking, molecular dynamics simulations, density functional theory, and covalent docking against the β-lactamases. We identified diosmin, hidrosmin, monoxuritin and solasulfone as β-lactamase inhibitors which are authorised for therapeutic use in humans. These medications interact in a remarkable variety of non-covalent ways with the conserved residues in the substrate-binding pocket of the β-lactamases. Diosmin has been identified as an inhibitor that binds covalently to the NDM-1 a class B metallo-betalactamase. After experimental validation and clinical demonstration, this study offers adequate evidence for the therapeutic use of these drugs for controlling multidrug resistance.Communicated by Ramaswamy H. Sarma.

In silico studies of alkaloids and their derivatives against N-acetyltransferase EIS protein from Mycobacterium tuberculosis

Antibiotic resistance against Mycobacterium tuberculosis (M.tb.) has been a significant cause of death worldwide. The Enhanced intracellular survival (EIS) protein of the bacteria is an acetyltransferase that multiacetylates aminoglycoside antibiotics, preventing them from binding to the bacterial ribosome. To overcome the EIS-mediated antibiotics resistance of M.tb., we compiled 888 alkaloids and derivatives from five different databases and virtually screened them against the EIS receptor. The compound library was filtered down to 87 compounds, which underwent additional analysis and filtration. Moreover, the top 15 most prominent phytocompounds were obtained after the drug-likeness prediction and ADMET screening. Out of 15, nine compounds confirmed the maximum number of hydrogen bond interactions and reliable binding energies during molecular docking. Additionally, the Molecular dynamics (MD) simulation of nine compounds showed the three most stable complexes, further verified by re-docking with mutated protein. The density functional theory (DFT) calculation was performed to identify the HOMO-LUMO energy gaps of the selected three potential compounds. Finally, our selected top lead compounds i.e., Alkaloid AQC2 (PubChem85634496), Nobilisitine A (ChEbi68116), and N-methylcheilanthifoline (ChEbi140673) demonstrated more favourable outcomes when compared with reference compounds (i.e., 39b and 2i) in all parameters used in this study. Therefore, we anticipate that our findings will help to explore and develop natural compound therapy against multi and extensively drug-resistant strains of M.tb.Communicated by Ramaswamy H. Sarma.

Novel phenoxyacetylthiosemicarbazide derivatives as novel ligands in cancer diseases

Numerous epidemiological studies report an increased risk of developing prostate cancer in patients with melanoma and an increased risk of developing melanoma in patients with prostate cancer. Based on our previous studies demonstrating the high anticancer activity of thiosemicarbazides with a phenoxy moiety, we designed nineteen phenoxyacetylthiosemicarbazide derivatives and four of them acting as potential dual-ligands for both cancers. All of the compounds were characterized by their melting points and 1H, 13C NMR and IR spectra. For selected compounds, X-ray investigations were carried out to confirm the synthesis pathway, identify the tautomeric form and intra- and intermolecular interaction in the crystalline state. The conformational preferences and electronic structure of molecules were investigated by theoretical calculation method. Lipophilicity of compounds (log kw) was determined using isocratic reversed phase/high pressure liquid chromatography RP-18. For the obtained compounds, in vitro tests were carried out on four melanoma cell lines (A375, G-361, SK-MEL2, SK-MEL28), four prostate cancer cell lines (PC-3, DU-145, LNCaP, VcaP) and a normal human fibroblast cell line (BJ). The most active compounds turned out to be F6. Cell cycle analysis, apoptosis detection, CellROX staining and mitochondrial membrane potential analysis were performed for the most sensitive cancer cells treated with most active compounds. DSC analysis was additionally performed for selected compounds to determine their purity, compatibility, and thermal stability. The process of prooxidation was proposed as a potential mechanism of anticancer activity.

Elucidation of kinetic and structural properties of eye lens ζ-crystallin: an in vitro and in silico approach

The Arabian Camelus dromedarius contains significant concentration of eye lens ζ-crystallin. This enzyme is also present in other life forms including humans, however in lower catalytic amounts. The recombinant camel ζ-crystallin was expressed in the E. coli BL21 (DE3) pLysS strain and purified using HisTrap column. The K_m of the enzyme for 9,10-phenanthrenequinone (9,10-PQ) substrate and NADPH cofactor was determined to be 11.66 and 50.93 µM, respectively. The V_max for 9,10-PQ and NADPH was obtained as 23.19 and 19.98 μM min^-1, respectively. The optimum activity of the purified enzyme was found to be at pH 6.0 and at 55 °C. Different physico-chemical parameters were analysed including instability index (II), aliphatic index (AI) and the GRAVY index to establish proper characterization. The sequence of the recombinant ζ-crystallin was subjected to homology modelling using SWISS-MODEL webserver followed by validation of the modelled target structure. The evaluation of the modelled ζ-crystallin was performed by several parameters including Ramachandran plot, Z-score values followed by molecular dynamics (MD) simulation. The cumulative analysis of the physico-chemical, quantitative, qualitative and the essential dynamics of simulation of ζ-crystallin and its complexes with 9,10-PQ and NADPH helped in verifying the acceptable quality and stability of the ζ-crystallin structure.Communicated by Ramaswamy H. Sarma.

Deciphering the competitive inhibition of dihydropteroate synthase by 8 marcaptoguanine analogs: enhanced potency in phenylsulfonyl fragments

The emergence of sulfa-drug resistance and reduced efficacy of pterin-based analogs towards Dihydropteroate synthase (DHPS) inhibition dictate a pressing need of developing novel antimicrobial agents for immune-compromised patients. Recently, a series of 8-Marcaptoguanin (8-MG) derivatives synthesized for 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (experimental K_D ∼ 100-.0.36) showed remarkable homology with the pteroic-acid and serve as a template for product antagonism in DHPS. The present work integrates ligand-based drug discovery techniques with structure-based docking, enhanced MD simulation, and MM/PBSA techniques to demonstrate the essential features of 8-MG analogs which make it a potent inhibitor for DHPS. The delicate balance in hydrophilic, hydrophobic substitutions on the 8-MG core is the crucial signature for DHPS inhibition. It is found that the dynamic interactions of active compounds are mainly dominated by consistent hydrogen bonding network with Asp 96, Asn 115, Asp 185, Ser 222, Arg 255 and π-π stacking, π-cation interactions with Phe 190, Lys 221. Further, two new 8-MG compounds containing N-phenylacetamide (compound S1, ΔG_bind-eff = -62.03 kJ/mol) and phenylsulfonyl (compound S3, ΔG_bind-eff = -71.29 kJ/mol) fragments were found to be the most potent inhibitor of DHPS, which stabilize the flexible pABA binding loop, thereby increasing their binding affinity. MM/PBSA calculation shows electrostatic energy contribution to be the principal component in stabilizing the inhibitors in the binding pocket. This fact is further confirmed by the higher energy barrier obtained in umbrella sampling for this class of inhibitors.

Molecular dynamics-based insight of VEGFR-2 kinase domain: a combined study of pharmacophore modeling and molecular docking and dynamics

BACKGROUND

Inhibition of vascular endothelial growth factor receptor 2 (VEGFR-2) tyrosine kinase by small molecules has become a promising target in the treatment of cancer.

OBJECTIVE

In this study, we approached pharmacophore modeling coupled with a structure-based virtual screening workflow to identify the potent inhibitors.

METHODS

The top selected hit compounds have been rescored using the MM/GBSA approach. To understand the molecular reactivity, electronic properties, and stability of those inhibitors, we have employed density functional theory and molecular dynamics. Following that, the best 21 hit compounds have been further post-processed with a Quantum ligand partial charge-based rescoring process and further validated by implementing molecular dynamics simulation.

RESULTS

The ten hit compounds have been hypothesized and considered as potent inhibitors of VEGFR-2 tyrosine kinase. This study also signifies the contribution of QM-based ligand partial charge, which is more accurate in predicting reliable free binding energy and filtering large ligand libraries to hit optimization, rather than assigning those of the force field-based method. From the binding pattern analysis of all the complexes, amino acids, such as Glu885, Cys919, Cys1045, Thr916, Thr919, and Asp1046, were found to have comprehensive interaction with the hit compounds.

CONCLUSION

Hence, this could prove to be useful as a potential inhibition site of the VEGFR-2 tyrosine kinase domain for future researchers. Moreover, this study also emphasizes the conformational changes upon ATP binding, based on either the receptor's rigidity or flexibility.

Discovery of imidazole-based GSK-3 inhibitors for transdifferentiation of human mesenchymal stem cells to neurons: A potential single-molecule neurotherapeutic foresight

The transdifferentiation of human mesenchymal stem cells (hMSC) to functional neurons is crucial for the development of future neuro-regenerative therapeutics. Currently, transdifferentiation of hMSCs to neurons requires a "chemical cocktail" along with neural growth factors. The role of the individual molecules present in a "chemical cocktail" is poorly understood and may cause unwanted toxicity or adverse effects. Toward, this goal, we have showcased the discovery of an imidazole-based "single-molecule" transdifferentiation initiator SG-145C. This discovery was achieved via screening of a small molecule library through extensive in silico studies to shortlist the best-fitting molecules. This discovery evolved through a careful selection to target Glycogen synthase kinase-3β (GSK-3β), which is one of the important proteins responsible for neurogenesis. Rigorous computational experiments, as well as extensive biological assays, confirmed that SG-145C has significant potential to transdifferentiate hMSCs to neurons. Interestingly, our results suggest that SG-145C can inhibit the proteasomal degradation of phosphorylated β-catenin, in turn promoting transdifferentiation of hMSCs into neurons via the Wnt pathway.

Identification of Novel Nrf2 Activator via Protein-ligand Interactions as Remedy for Oxidative Stress in Diabetes Mellitus

Background:

Oxidative stress is a significant player in the pathogenesis of diabetes mellitus and the Kelch-like ECH-associated protein1/nuclear factor erythroid 2-related factor 2/antioxidant response element (Keap1/Nrf2/ARE) signaling pathway serves as the essential defense system to mitigate oxidative stress. Nrf2 is responsible for the mitigation of oxidative stress while Keap1 represses Nrf2’s activation upon binding. Identification of Nrf2 activators has started to pick up enthusiasm as they can be used as therapeutic agents against diabetes mellitus. One of the ongoing mechanisms in the activation of Nrf2 is to disrupt Keap1/Nrf2 protein-protein interaction. This study aimed at using computational analysis to screen natural compounds capable of inhibiting Keap1/Nrf2 protein-protein interaction.

Methods:

A manual curated library of natural compounds was screened against crystal structure of Keap1 using glide docking algorithm. Binding free energy of the docked complexes, and adsorption, digestion, metabolism and excretion (ADME) properties were further employed to identify the hit compounds. The bioactivity of the identified hit against Keap1 was predicted using quantitative structure-activity relationship (QSAR) model.

Results:

A total of 7 natural compounds (Compound 222, 230, 310, 208, 210, 229 and 205) identified from different medicinal plants were found to be potent against Keap1 based on their binding affinity and binding free energy. The internal validated model kpls_radial_30 with R2 of 0.9109, Q2 of 0.7287 was used to predict the compounds’ bioactivities. Compound 205 was considered as the ideal drug candidate because it showed moderation for ADME properties, had predicted pIC50 of 6.614 and obeyed Lipinski’s rule of five.

Conclusion:

This study revealed that Compound 205, a compound isolated from Amphipterygium adstringens is worth considering for further experimental analysis.

Disruption of DYRK1A-induced hyperphosphorylation of amyloid-beta and tau protein in Alzheimer's disease: An integrative molecular modeling approach

Alzheimer's disease (AD) is a neurological disorder caused by the abnormal accumulation of hyperphosphorylated proteins. Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a dual phosphorylation enzyme which phosphorylates the amyloid-β (Aβ) and neurofibrillary tangles (NFTs). A high throughput virtual screening approach was applied to screen a library of 98,071 compounds against DYRK1A using different programs including AutoDock Vina, Smina, and idock. Based on the binding affinities, we selected 330 compounds for absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. Various pharmacokinetics parameters were predicted using the admetSAR server, and based on the pharmacokinetics results, 14 compounds were selected for cross-docking analysis using AutoDock. Cross-docking analysis revealed four compounds, namely, ZINC3843365 (-11.07 kcal/mol^-1), ZINC2123081 (-10.93 kcal/mol^-1), ZINC5220992 (-10.63 kcal/mol^-1), and ZINC68569602 (-10.35 kcal/mol^-1), which had the highest negative affinity scores compared to the 10 other molecules analyzed. Density functional theory (DFT) analysis was conducted for all the four top-ranked compounds. The molecular interaction stability of these four compounds with DYRK1A has been evaluated using molecular dynamics (MD) simulations on 100 nanoseconds followed by principal component analysis (PCA) and binding free energy calculations. The Gibbs free energy landscape analysis suggested the metastable state and folding pattern of selected docking complexes. Based on the present study outcome, we propose four antagonists, viz., ZINC3843365, ZINC2123081, ZINC5220992, and ZINC68569602 as potential inhibitors against DYRK1A and to reduce the amyloid-β and neurofibrillary tangle burden. These screened molecules can be further investigated using a number of in vitro and in vivo experiments.

A comparative study based on activity, conformation and computational analysis on the inhibition of human salivary aldehyde dehydrogenase by phthalate plasticizers: Implications in assessing the safety of packaged food items

Phthalate plasticizers are commonly used in various consumer-end products. Human salivary aldehyde dehydrogenase (hsALDH) is a detoxifying enzyme which defends us from the toxic aldehydes. Here, the effect of phthalates [Di-2-ethylhexyl phthalate (DEHP), Diethyl phthalate (DEP) and Dibutyl phthalate (DBP)] on hsALDH has been investigated. These plasticizers inhibited hsALDH, and the IC₅₀ values were 0.48 ± 0.04, 283.20 ± 0.09 and 285.00 ± 0.14 μM for DEHP, DEP and DBP, respectively. DEHP was the most potent inhibitor among the three plasticizers. They exhibited mixed-type linear inhibition with inclination towards competitive-non-competitive inhibition. They induced both tertiary and secondary structural changes in the enzyme. Quenching of intrinsic hsALDH fluorescence in a constant manner was observed with a binding constant (K_b) of 8.91 × 10⁶, 2.80 × 10⁴, and 1.31 × 10⁵ M^-1, for DEHP, DEP and DBP, respectively. Computational analysis showed that these plasticizers bind stably in the proximity of hsALDH catalytic site, reciprocating via non-covalent interactions with some of the amino acids which are evolutionary conserved. Therefore, exposure to these plasticizers inhibits hsALDH which increases the risk of aldehyde induced toxicity, adversely affecting oral health. The study has implications in assessing the safety of packaged food items which utilize phthalates.

1,2,5-Thiadiazole Scaffold: A review on recent progress in biological activities

BACKGROUND

Thiadiazoles can be considered as the privileged scaffold having diverse pharmacological potentials such as antihypertensive, anti-HIV, antimicrobials, antileishmanial agents, etc. In particular, 1,2,5-thiadiazoles and their fused analogues are subjects of fast-growing interest due to their higher significance in the fields of biomedicine and material sciences.

OBJECTIVE

This study aims to collect detailed medicinal information about aspects of 1,2,5-thiadiazole.

METHODS

A systemic search has been carried out using PubMed, Google Scholar, CNKI, etc., for relevant studies having the keyword, '1,2,5-thiadiazole'.

RESULTS AND CONCLUSION

In this mini-review, we have covered known procedures of the synthesis and explored in detail all known advancements of this scaffold concerning to its biological activities.

Computer-assisted evaluation of plant-derived β-secretase inhibitors in Alzheimer’s disease

Background

Alzheimer’s disease (AD) is a progressive neurodegenerative age-related dementia that results in memory loss of elderly people. Many hypotheses have been formally articulated till now to decipher the pathogenesis of this disease. According to the compelling amyloidogenic hypothesis, β-secretase is a key regulatory enzyme in AD development and is therefore considered as one of the major targets for the development of drugs to treat AD. In this study, 40 plant-derived phytocompounds, proven to have β-secretase inhibitory activity in different laboratory experiments, were evaluated using computational approaches in order to identify the best possible β-secretase inhibitor(s).

Results

Amentoflavone (IFD score: − 7.842 Kcal/mol), Bilobetin (IFD score: − 7.417 Kcal/mol), and Ellagic acid (IFD score: − 6.923 Kcal/mol) showed highest β-secretase inhibitory activities with high binding affinity among all the selected phytocompounds and interacted with key amino acids, i.e., Asp32, Tyr71, and Asp228 in the catalytic site of β-secretase. Moreover, these three molecules exhibited promising results in different drug potential assessment experiments and displayed signs of correlation with significant pharmacological and biological activities.

Conclusion

Amentoflavone, Biolbetin, and Ellagic acid could be investigated further in developing β-secretase-dependent drug for the effective treatment of AD. However, additional in vivo and in vitro experiments might be required to strengthen the findings of this experiment.

Identification of the most potent acetylcholinesterase inhibitors from plants for possible treatment of Alzheimer’s disease: a computational approach

Background

Being one of the rapidly growing dementia type diseases in the world, Alzheimer’s disease (AD) has gained much attention from researchers in the recent decades. Many hypotheses have been developed that describe different reasons for the development of AD. Among them, the cholinergic hypothesis depicts that the degradation of an important neurotransmitter, acetylcholine by the enzyme acetylcholinesterase (AChE), is responsible for the development of AD. Although, many anti-AChE drugs are already available in the market, their performance sometimes yields unexpected results. For this reason, research works are going on to find out potential anti-AChE agents both from natural and synthetic sources. In this study, 50 potential anti-AChE phytochemicals were analyzed using numerous tools of bioinformatics and in silico biology to find out the best possible anti-AChE agents among the selected 50 ligands through molecular docking, determination of the druglikeness properties, conducting the ADMET test, PASS and P450 site of metabolism prediction, and DFT calculations.

Result

The predictions of this study suggested that among the selected 50 ligands, bellidifolin, naringenin, apigenin, and coptisine were the 4 best compounds with quite similar and sound performance in most of the experiments.

Conclusion

In this study, bellidifolin, naringenin, apigenin, and coptisine were found to be the most effective agents for treating the AD targeting AChE. However, more in vivo and in vitro analyses are required to finally confirm the outcomes of this research.

Destabilization of Alzheimer's Aβ42 protofibrils with acyclovir, carmustine, curcumin, and tetracycline: insights from molecular dynamics simulations

Among the neurodegenerative diseases, one of the most common dementia is Alzheimer's disease (AD).

Thiadiazole derivatives as anticancer agents

In spite of substantial progress made toward understanding cancer pathogenesis, this disease remains one of the leading causes of mortality. Thus, there is an urgent need to develop novel, more effective anticancer therapeutics. Thiadiazole ring is a versatile scaffold widely studied in medicinal chemistry. Mesoionic character of this ring allows thiadiazole-containing compounds to cross cellular membrane and interact strongly with biological targets. Consequently, these compounds exert a broad spectrum of biological activities. This review presents the current state of knowledge on thiadiazole derivatives that demonstrate in vitro and/or in vivo efficacy across the cancer models with an emphasis on targets of action. The influence of the substituent on the compounds' activity is depicted. Furthermore, the results from clinical trials assessing thiadiazole-containing drugs in cancer patients are summarized.

Analysis of plant-derived phytochemicals as anti-cancer agents targeting cyclin dependent kinase-2, human topoisomerase IIa and vascular endothelial growth factor receptor-2

Cancer is caused by a variety of pathways, involving numerous types of enzymes. Among them three enzymes i.e. Cyclin-dependent kinase-2 (CDK-2), Human topoisomerase IIα, and Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2) are three of the most common enzymes that are involved in the cancer development. Although many chemical drugs are already available in the market for cancer treatment, plant sources are known to contain a wide variety of agents that are proved to possess potential anticancer activity. In this experiment, total thirty phytochemicals were analyzed against the mentioned three enzymes using different tools of bioinformatics and in silico biology like molecular docking study, drug likeness property experiment, ADME/T test, PASS prediction, and P450 site of metabolism prediction as well as DFT calculation to determine the three best ligands among them that have the capability to inhibit the mentioned enzymes. From the experiment, Epigallocatechin gallate was found to be the best ligand to inhibit CDK-2, Daidzein showed the best inhibitory activities towards the Human topoisomerase IIα, and Quercetin was predicted to be the best agent against VEGFR-2. They were also predicted to be quite safe and effective agents to treat cancer. However, more in vivo and in vitro analyses are required to finally confirm their safety and efficacy in this regard.

In Silico Computations of Selective Phytochemicals as Potential Inhibitors Against Major Biological Targets of Diabetes Mellitus

BACKGROUND

In the past few years, several developments have been made to understand and control the complications and harmful side-effects associated with the disorder diabetes mellitus (DM). Many new steps have been taken in a better understanding of the pathophysiology of the disease. With the advancement in the field of medical sciences, various novel therapies have been developed to efficiently control the pathological effects of diabetes mellitus. Recently, phytochemicals possessing various medicinal properties have opened up a new vast range of opportunities to design novel therapeutic drugs against diabetes mellitus.

OBJECTIVE

The present study aims to identify and screen phytochemicals as potent and novel inhibitors against diabetes mellitus.

METHODS

Three major biological targets of diabetes mellitus named Cytochrome P450, glycogen synthase kinase and PPARγ are targeted using phytochemicals by performing pharmacological properties prediction, molecular docking and density functional theory studies.

RESULTS

Out of 108 phytochemicals, 20, 12 and 3 phytochemicals showed higher binding affinity values as compared to chemically synthesized drugs against cytochrome P450, glycogen synthase kinase and PPARγ, respectively.

CONCLUSION

The screened phytochemicals have strong inhibitory potential against diabetes mellitus and in future, these compounds, holding immense potential, can be considered as candidate drugs for treating diabetes mellitus.

Combining in silico and in vitro approaches to identification of potent inhibitor against phospholipase A2 (PLA2)

Phospholipase A2 (PLA2) is the main constituent of snake venom. PLA2 enzymes catalyze the Ca²⁺ dependent hydrolysis of 2-acyl ester bonds of 3-sn-phospholipids, releasing fatty acids and lysophospholipids. Inside the body of the victim, PLA2 from snake venom induces either direct or indirect pathophysiological effects, including anticoagulant, inflammatory, neurotoxic, cardiotoxic, edematogenic, and myotoxic activities. Therefore, there is a need to find the potential inhibitors against PLA2 responsible for snakebite. In this study, we employed in silico and in vitro methods to identify the potential inhibitor against PLA2. Virtual screening and molecular docking studies were performed to find potent inhibitor against PLA2 using Traditional Chinese Medicine Database (TCM). Based on these studies, Scutellarin (TCM3290) was selected and calculated by density functional theory calculation at B3LYP/6-31G**⁺⁺ level to explore the stereo-electronic features of the molecule. Further, molecular docking and DFT of Minocycline was carried out. Quantum polarized ligand docking was performed to optimize the geometry of the protein-ligand complexes. The protein-ligand complexes were subjected to molecular dynamics simulation and binding free energy calculations. The residence time of a protein-ligand complex is a critical parameter affecting natural influences in vitro. It is nonetheless a challenging errand to expect, regardless of the accessibility of incredible PC assets and a large variety of computing procedures. In this metadynamics situation, we used the conformational flooding technique to deal with rank inhibitors constructions. The systematic free energy perturbation (FEP) protocol and calculate the energy of both complexes. Finally, the selected compound of TCM3290 was studied in vitro analysis such as inhibition of PLA2 activity, hyaluronidase activity and fibrinogenolytic activity. The TCM3290 had a more binding affinity compare to Minocycline, and interacted with the key residues of TYR63 and GLY31. DFT represented the highest HOMO and LUMO energy of 0.15146 eV. MD simulation with 100 ns proved that an inhibitor binding mode is more stable inside the binding site of PLA2. In vitro analysis shows that TCM3290 significantly neutralized by PLA2. The above observations confirmed that Scutellarin (TCM3290) had a potent snake venom neutralizing capacity and could hypothetically be used for therapeutic drives of snakebite envenomation.

Design, synthesis and ADMET prediction of bis-benzimidazole as anticancer agent

A new series of bis-benzimidazole clubbed with primary amine (3i-iii) and aromatic aldehydes (4i-ix) were design and synthesize with an intention to search an anticancer lead compound under microwave irradiation in good yields. Further, the spectral characterization of synthetic compounds were done with modern instrumental techniques such as FTIR, NMR (¹H and ¹³C), MS and elemental analysis. Anticancer activities of synthesized compounds were investigated at National Cancer Institute (NCI) against NCI 60 cell line panel, results showed good to notable anticancer activity. With the help of molinspiration, drug like properties and bioactivity score for drug targets of synthetic compounds were predicted and found to obey the Lipinski's rule, result indicates that the derivatives are orally active molecules. Osiris property explorer was used for the prediction of drug relevant properties and toxicity of synthetic compounds. Pre ADMET and Lazar toxicity was also used to estimate ADME and toxicity of synthetic compounds. Two compounds, 4i [(Z)-2-((1H-benzo[d]imidazol-2-yl) methyl)-1-(1H-benzo[d]imidazol-2-yl)-3-(thiophen-2-yl) prop-2-en-1-one] and 4iii [(Z)-2-((1H-benzo[d]imidazol-2-yl) methyl)-1-(1H-benzo [d] imidazol-2-yl)-3-(1H-pyrrol-2-yl)prop-2-en-1-one] were exhibited highest drug score and emerged as lead compounds and motivates for further development of more effective and safer compounds.

Computer-aided identification of lead compounds as Staphylococcal epidermidis FtsZ inhibitors using molecular docking, virtual screening, DFT analysis, and molecular dynamic simulation

In an effort to face the multiple drug-resistant bacteria, various approaches have been discovered to design potent compounds and search new targets through computational design tools. With an aim to identify selective inhibitors against filamentous temperature-sensitive mutant Z (FtsZ), a library of Phase database compounds have been virtually screened. High-throughput virtual screening of compounds against Staphylococcal epidermidis FtsZ protein (4M8I) was performed using three sequential docking modes like high-throughput virtual screening, Glide standard precision, followed by Glide extra precision. Four top-ranked compounds were selected from molecular mechanics-generalized Born surface area (MM-GBSA) binding energy with better predicted free binding energies of - 89.309, - 54.382, - 53.667, and - 52.133 kcal/mol, respectively. It is also showed that the contribution of van der Waals and electrostatic solvation energy terms are playing a major part to make the hit molecule (T6288784) binding to S. epidermidis FtsZ protein. The result of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and energy gap analysis predicts the molecular reactivity and stability of hit molecules. Subsequently, Lipinski's rule of five and properties of absorption, distribution, metabolism, and excretion (ADME) were to calculate their bioavailability. The average binding energy - 9.67 kcal/mol of the best proposed hit molecule (T6288784) was found with half-maximal inhibitory concentration (IC50) value to be 75.53 nM. A 15-ns molecular dynamics simulation study revealed the stable conformation of hit molecule. On a wide-range research discipline, in silico studies of our proposed compound confirm promising results and can be successfully used towards the development of novel FtsZ inhibitor with better binding affinity. Graphical Abstract.

Synthesis, Antioxidant and Anti-inflammatory Activities of 5-((styrylsulfonyl) methyl)-1,3,4-Oxadiazol / Thiadiazol-2-amine Derivatives

Background:

A new class of 5-(styrylsulfonylmethyl)-1,3,4-oxadiazol-2-amine and 5- (styrylsulfonylmethyl)-1,3,4-thiadiazol-2-amine derivatives were prepared by derivatization of amino function.

Methods:

All the synthesized compounds were tested for antioxidant and anti-inflammatory activities.

Results:

The 2-amino-3-chloro-N-(5-(4-methylstyrylsulfonylmethyl)-1,3,4-oxadiazol-2-yl)-propanamide (12b) and 3-chloro-N-(5-(4-methylstyrylsulfonylmethyl)-1,3,4-oxadiazol-2-yl)-butanamide (14b) displayed significant antioxidant activity, greater than the standard Ascorbic acid.

Conclusion:

Moreover, 12b and 14b also exhibited promising anti-inflammatory activity

Exploring the potent inhibitors and binding modes of phospholipase A2 through in silico investigation

Snake venom of Naja naja comprises of several types of enzymes, and among them, water-soluble proteolytic enzyme, phospholipase A2 (PLA₂), is noteworthy for its numerous adverse effects, such as cytotoxicity, cardiotoxicity, hemolytic, anti-coagulant, and hypotensive effects, including being highly potent as a neurotoxin. Limited anti-venom therapy (with their lower efficacy) has attracted considerable pharmacological interest to develop potent inhibitors of PLA₂. Thus, 34 experimentally proven and diverse synthetic inhibitors of PLA₂ were screened primarily on the basis of Glide extra precision docking and MM-GBSA rescoring function. Then, ten potential hits were subjected to induced fit docking, in which top three potential inhibitors were considered, and those were found to interact with Ca²⁺, disulfide binding site, and phosphatidylcholine activation sites, thereby, possibly disrupting the catalytic activity of Ca²⁺ as well as the inflammatory functions of PLA₂. These compounds showed positive remarks on various physiochemical properties and pharmacologically relevant descriptors. Gap energy and thermodynamic properties were investigated by employing density functional theory for all compounds to understand their chemical reactivity and thermodynamic stability. Molecular dynamics simulation was performed for 100 ns in order to evaluate the stability and binding modes of docked complexes, and the energy of binding was calculated through MM-PBSA analysis. On the whole, the proposed compounds could be used for targeted inhibition. Communicated by Ramaswamy H. Sarma.

Identification of potential drugs targeting L,L-diaminopimelate aminotransferase of Chlamydia trachomatis: An integrative pharmacoinformatics approach

Chlamydia trachomatis (C.t) is a gram-negative obligate intracellular bacteria, which is a major causative of infectious blindness and sexually transmitted diseases. A surge in multidrug resistance among chlamydial species has posed a challenge to adopt alternative drug targeting strategies. Recently, in C.t, L,L-diaminopimelate aminotransferase (CtDAP-AT) is proven to be a potential drug target due its essential role in cell survival and host nonspecificity. Hence, in this study, a multilevel precision-based virtual screening of CtDAP-AT was performed to identify potential inhibitors, wherein, an integrative stringent scoring and filtration were performed by coupling, glide docking score, binding free energy, ADMET (absorption, distribution, metabolism, and excretion, toxicity) prediction, density functional theory (quantum mechanics), and molecular dynamics simulation (molecular mechanics). On cumulative analysis, NSC_5485 (1,3-bis((7-chloro-4-quinolinyl)amino)-2-propanol) was found to be the most potential lead, as it showed higher order significance in terms of binding affinity, bonded interactions, favorable ADMET, chemical reactivity, and greater stabilization during complex formation. This is the first report on prioritization of small molecules from National Cancer Institute (NCI) and Maybridge data sets (341 519 compounds) towards targeting CtDAP-AT. Thus, the proposed compound shall aid in effective combating of a broad spectrum of C.t infections as it surpassed all the levels of prioritization.

Multiple 3D-QSAR modeling, e-pharmacophore, molecular docking, and in vitro study to explore novel AChE inhibitors

Ligand-based and energy-optimized structure-based approaches were considered to obtain excellent candidates as AChE inhibitors. The known AChE inhibitors were utilized to develop a pharmacophore hypothesis, HPRRR and X-ray crystallographic structures of AChE were used to produce three e-pharmacophore hypotheses viz. AHHRR, AHRR, and DHRR. Based on in silico approaches, we came across eight structurally diverse hits as non-competitive AChE inhibitors with good ADME properties. The best four hits, ZINC20592007, ZINC05354646, ZINC20649934, and ZINC39154782 were non-toxic, neuroprotective, and were selective AChE inhibitors (IC50 values 482 ± 1.88 nM, 580 ± 1.63 nM, 854 ± 2.65 nM, and 636 ± 1.79 nM respectively). The hits showed non-competitive inhibition of AChE at PAS site with attractive K i values (0.21 ± 0.027 μM, 0.27 ± 0.064 μM, 0.3 ± 0.018 μM, and 0.28 ± 0.032 μM for ZINC20592007, ZINC05354646, ZINC20649934, and ZINC39154782 respectively), and increased the cholinergic activity as well as inhibited Aβ aggregation.

Molecular dynamics and quantum chemistry-based approaches to identify isoform selective HDAC2 inhibitor - a novel target to prevent Alzheimer's disease

Histone deacetylase 2 (HDAC2) is an emerging target of Alzheimer's disease. Four featured pharmacophore model (ADRR) with one H-bond acceptor (A), one H-bond donor (D), and two aromatic rings (R) was generated using experimentally reported compounds, ((E-5[3-benzenesulfonamido) phenyl]-N-hydroxypent-2-en-4-ynamide)) and (N'-hydroxy-N-phenyloctanediamide) with IC₅₀ values of 0.16 ± 0.11 nM and 62 ± 0.15 nM, respectively. Quantum Polarized Ligand Docking and Binding Free Energy calculation was performed for the top three identified leads RH01652, JFD02573, and HTS00800 from HitFinder database. RH01652 (methyl 2-[({5-[(benzoylamino) methyl]-2-thienyl} sulfonyl) amino]-3-(1H-indol-3-yl) propanoate) with docking score (-12.62 kcal/mol) and binding free energy (-75.27 kcal/mol), shows good binding affinity. RH01652 interacts with Gly154, His183, Glu208, and Phe210 with four H-bonds and stabilized by π-π interactions with His146, Tyr209, and Phe210. DFT studies at B3LYP level with 6-31G* basis set for the lead RH01652 reveals low band gap/ΔE (E_HOMO-E_LUMO) of -0.16 eV, which illustrates good reactivity of the lead. MD simulation studies (40 ns) was performed to confirm the stability of lead binding. Comparative molecular docking studies of the lead RH01652 with class I HDACs (HDAC1, HDAC2, HDAC3, and HDAC8) shows higher binding affinity towards HDAC2. Thus, lead RH01652 could serve as template to design novel and potent inhibitor of HDAC2.

Identification of natural inhibitors of Bcr-Abl for the treatment of chronic myeloid leukemia

Chronic myeloid leukemia (CML) is a clonal myeloproliferative disorder of the hematopoietic stem cells, characterized at the molecular level by the bcr/abl gene rearrangement. Even though targeting the fusion gene product Bcr-Abl protein is a successful strategy, development of drug resistance and that of drug intolerance are currently the limitations for Bcr-Abl-targeted CML therapy. With an aim to develop natural Bcr-Abl inhibitors, we performed virtual screening (VS) of ZINC natural compound database by docking with Abl kinase using Glide software. Two natural inhibitors ZINC08764498 (hit1) and ZINC12891610 (hit2) were selected by considering their high Glide docking score and critical interaction with the hinge region residue Met-318 of Abl kinase. The reactivity of the two molecules was assessed computationally by density functional theory calculations. Further, the conformational transition, hydrogen bond interactions, and the binding energies were investigated during 10-ns molecular dynamics simulation of the Abl-hit complex. When tested in vitro, hit1 compared to hit2 showed selective inhibition of cell proliferation and induction of apoptosis in Bcr-Abl-positive K-562 leukemia cells. In summary, our results demonstrate that ZINC08764498, a coumarin derivative identified through VS, is a potential natural inhibitor for the treatment of CML.

Opening the door to the development of novel Abl kinase inhibitors

The discovery of the importance of kinase activity and its relationship to the emergence and proliferation of cancer cells, due to changes in normal physiology, opened a remarkable pathway for the treatment of chronic myelogenous leukemia through intense search of drug candidates. Six Abl kinase inhibitors have received the US FDA approval as chronic myelogenous leukemia treatment, and continuous efforts in obtaining new, more effective and selective molecules are being carried out. Herein we discuss the mechanisms of Abl inhibition, structural features and ligand/protein interactions that are important for the design of new Abl kinase inhibitors. This review provides a broad overview of binding mode predictions, through molecular docking, which can be an approach to discover novel Abl kinase inhibitors.

Trimodal Therapy: Combining Hyperthermia with Repurposed Bexarotene and Ultrasound for Treating Liver Cancer

Repurposing of existing cancer drugs to overcome their physical limitations, such as insolubility, represents an attractive strategy to achieve enhanced therapeutic efficacy and broaden the range of clinical applications. Such an approach also promises to offer substantial cost savings in drug development efforts. Here we repurposed FDA-approved topical agent bexarotene (Targretin), currently in limited use for cutaneous manifestations of T-cell lymphomas, and re-engineer it for use in solid tumor applications by forming self-assembling nanobubbles. Physico-chemical characterization studies of the novel prodrug nanobubbles demonstrated their stability, enhanced target cell internalization capability, and highly controlled release profile in response to application of focused ultrasound energy. Using an in vitro model of hepatocellular carcinoma and an in vivo large animal model of liver ablation, we demonstrate the effectiveness of bexarotene prodrug nanobubbles when used in conjunction with catheter-based ultrasound, thereby highlighting the therapeutic promise of this trimodal approach.

Identification of novel tyrosine kinase inhibitors for drug resistant T315I mutant BCR-ABL: a virtual screening and molecular dynamics simulations study

BCR-ABL tyrosine kinase plays a major role in the pathogenesis of chronic myeloid leukemia (CML) and is a proven target for drug development. Currently available drugs in the market are effective against CML; however, side-effects and drug-resistant mutations in BCR-ABL limit their full potential. Using high throughput virtual screening approach, we have screened several small molecule databases and docked against wild-type and drug resistant T315I mutant BCR-ABL. Drugs that are currently available, such as imatinib and ponatinib, were also docked against BCR-ABL protein to set a cutoff value for our screening. Selected lead compounds were further evaluated for chemical reactivity employing density functional theory approach, all selected ligands shows HLG value > 0.09900 and the binding free energy between protein-ligand complex interactions obtained was rescored using MM-GBSA. The selected compounds showed least ΔG score -71.53 KJ/mol to maximum -126.71 KJ/mol in both wild type and drug resistant T315I mutant BCR-ABL. Following which, the stability of the docking complexes were evaluated by molecular dynamics simulation (MD) using GROMACS4.5.5. Results uncovered seven lead molecules, designated with Drug-Bank and PubChem ids as DB07107, DB06977, ST013616, DB04200, ST007180 ST019342, and DB01172, which shows docking scores higher than imatinib and ponatinib.