Exploration of Computational Aids for Effective Drug Designing and Management of Viral Diseases: A Comprehensive Review.

BACKGROUND: Microbial diseases, specifically originating from viruses are the major cause of human mortality all over the world. The current COVID-19 pandemic is a case in point, where the dynamics of the viral-human interactions are still not completely understood, making its treatment a case of trial and error. Scientists are struggling to devise a strategy to contain the pandemic for over a year and this brings to light the lack of understanding of how the virus grows and multiplies in the human body. METHODS: This paper presents the perspective of the authors on the applicability of computational tools for deep learning and understanding of host-microbe interaction, disease progression and management, drug resistance and immune modulation through in silico methodologies which can aid in effective and selective drug development. The paper has summarized advances in the last five years. The studies published and indexed in leading databases have been included in the review. RESULTS: Computational systems biology works on an interface of biology and mathematics and intends to unravel the complex mechanisms between the biological systems and the inter and intra species dynamics using computational tools, and high-throughput technologies developed on algorithms, networks and complex connections to simulate cellular biological processes. CONCLUSION: Computational strategies and modelling integrate and prioritize microbial-host interactions and may predict the conditions in which the fine-tuning attenuates. These microbial-host interactions and working mechanisms are important from the aspect of effective drug designing and fine- tuning the therapeutic interventions.

Mixed Ligand-metal Complexes of 2-(butan-2-ylidene) Hydrazinecarbothioamide- Synthesis, Characterization, Computer-Aided Drug Character Evaluation and in vitro Biological Activity Assessment.

BACKGROUND: Mixed ligand-metal complexes are efficient chelating agents because of their flexible donor ability. Mixed ligand complexes containing hetero atoms sulphur, nitrogen and oxygen have been probed for their biological significance. METHODS: Nine mixed ligand-metal complexes of 2-(butan-2-ylidene) hydrazinecarbothioamide (2- butanone thiosemicarbazone) with pyridine, bipyridine and 2-picoline as co-ligands were synthesized with Cu, Co and Zn salts. The complexes were tested against MDA-MB231 (MDA) and A549 cell lines. Antibacterial activity was tested against Staphylococcus aureus and Escherichia coli. The drug character of the complexes was evaluated on parameters viz. physicochemical properties, bioactivity scores, toxicity assessment and Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) profile using various automated softwares. Molecular docking was performed against Ribonucleotide Reductase (RR) and topoisomerase II (topo II). RESULTS: The mixed ligand-metal complexes were synthesized by condensation reaction for 4-5 h. The characterization was done by elemental analysis, 1H-NMR, FT-IR, molar conductance and UV spectroscopic techniques. Molecular docking results showed that [Cu(C5H11N3S)(py)2(CH3COO)2], [Zn(C5H11N3S)(bpy)(SO4)] and [Zn(C5H11N3S)(2-pic)2(SO4)] displayed the lowest binding energies with respect to RR. Against topo II [Cu(C5H11N3S)(py)2(CH3COO)2], [Cu(C5H11N3S)(bpy)(CH3COO)2] and [Zn(C5H11N3S)(2-pic)2(SO4)] had the lowest energies. The druglikness assessment was done using Leadlikeness and Lipinski's rules. Not more than two violations were obtained in case of each filtering rule showing drug-like character of the mixed ligand complexes. Some of the complexes exhibited positive bioactivity scores and almost all the complexes were predicted to be safe with no hazardous effects as predicted by the toxicity assessment. Ames test predicted the non-mutagenic nature of the complexes. CONCLUSION: In vitro activity evaluation showed that [Zn(C5H11N3S)(py)2(SO4)], [Co(C5H11N3S(bpy) (Cl)2] and [Cu(C5H11N3S)(2-pic)2(CH3COO)2] were active against MDA. Against A549 [Co(C5H11N3S)(py)2(Cl)2], [Cu(C5H11N3S)(py)2(CH3COO)2] and [Co(C5H11N3S(bpy)(Cl)2] were active. Antibacterial evaluation showed that [Co(C5H11N3S)(bpy)(Cl)2], [Zn(C5H11N3S)(2-pic)2(SO4)] and [Cu(C5H11N3S)(2-pic)2(CH3COO)2] were active against S. aureus. Against E. coli, [Zn(C5H11N3S)(2- pic)2(SO4)] showed activity at 18-20 mg dose range.

Withdrawal Notice: Computational Druglikeness Assessment, Synthesis, Characterization and In vitro Biological Activity Evaluation of some Novel Mixed Metal Complexes of 2-(butan-2-ylidene) Hydrazinecarbothioamide

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Computational Drug Designing and Prediction Of Important Parameters Using in silico Methods- A Review.

BACKGROUND: Computational or in silico studies are undertaken to assess the drug like properties of lead compounds. These studies help in fast prediction of relevant properties. OBJECTIVE: Through this review, an effort is made to encapsulate some of the important parameters which should be met by a compound for it to be considered as a potential drug candidate along with an overview of automated softwares which can be used for making various predictions. METHODS: Drug uptake, its absorption, evacuation and associated hazardous effects are important factors for consideration in drug designing and should be known in early stages of drug development. Several important physicochemical properties like molecular weight, polar surface area (PSA), molecular flexibility etc. have to be taken into consideration in drug designing. Toxicological assessment is another important aspect of drug discovery which predicts the safety and adverse effects of a drug. RESULTS: Additionally, bioactivity scores of probable drug leads against various human receptors can also be predicted to evaluate the probability of them to act as a potential drug candidate. The in vivo biological targets of a molecule can also be efficiently predicted by molecular docking studies. CONCLUSION: Some important software like iGEMDOCK, AutoDock, OSIRIS property explorer, Molinspiration, MetaPrint2D, admetSAR and their working methodology and principle of working have been summarized in this review.

Computer-aided drug design and virtual screening of targeted combinatorial libraries of mixed-ligand transition metal complexes of 2-butanone thiosemicarbazone.

The present paper deals with in silico evaluation of 32 virtually designed transition metal complexes of 2-butanone thiosemicarbazone and N,S,O containing donor hetero-ligands namely py, bpy, furan, thiophene, 2-picoline, 1,10-phenanthroline, piperazine and liquid ammonia. The complexes were designed with a view to assess their potential anticancer, antioxidant and antibacterial activity. The absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of the chosen ligands were calculated by admetSAR software. Metabolic sites of different ligands likely to undergo metabolism were predicted using Metaprint 2D. The proposed complexes were also evaluated for their drug-like quality based on Lipinski's, Veber, Ghose and leadlikeness filters. Druglikeness and toxicity potential were predicted by OSIRIS property explorer. The pharmacokinetic properties and bioactivity scores were calculated by Molinspiration tool. Bioactivity scores of the complexes were predicted for drug targets including enzymes, nuclear receptors, kinase inhibitors, G-protein coupled receptor ligands and ion channel modulators. Molecular docking of selected Fe(II) mixed-ligand complexes was performed using AutoDock version 4.2.6 and i-GEMDOCK version 2.1 with two target proteins namely Ribonucleotide reductase (RR) and Topoisomerase II (Topo II). The results were compared with three standard reference drugs viz. Doxorubicin HCl, Letrozole (anticancer) and Tetracycline (antibiotic). Multivariate data obtained were analyzed using principal component analysis (PCA) for visualization and projection as scatter and 3D plots. Positive results obtained for hetero-ligands using admetSAR version 1.0 indicated good absorption and transport kinetics of the hetero-ligand complexes through the human intestine and blood-brain barrier. The hetero-ligands were predicted to have no associated mutagenic effect(s) also. However, none of the hetero-ligands was predicted to be Caco-2 (human colon cancer cell line) permeable. Most of the hetero-ligands and the parent ligand (2-butanone thiosemicarbazone) were predicted to undergo Phase-I metabolism prior to excretion using MetaPrint2D software. Pharmacokinetic evaluation of the proposed complexes revealed that all complexes displayed drug-like character and were predicted to have no apparent toxic side-effects. All the proposed complexes showed moderate to good biological activity scores (-5.0 to 0.0). Mixed complexes with bpy, 2-picoline and 1,10-phenanthroline showed significant bioactivity scores (as enzyme inhibitors) in the range 0.02-0.13. Likewise, good docking scores were obtained for Fe (II) complexes with the same ligands. [FeL(2-pic)2] displayed the lowest binding energy (-6.47 kcal/mol) with respect to Topo II followed by [FeL(py)2] (-6.14 kcal/mol) as calculated by AutoDock version 4.2.6. With respect to binding with RR, [FeL(2--pic)2] again displayed the lowest binding energy (-7.21 kcal/mol) followed by [FeL(py)2] (-5.96 kcal/mol). On the basis of docking predictions and various other computational evaluations, four mixed-ligand complexes of Fe in +2 oxidation state with py, bpy, 2--picoline and 1,10-phenanthroline were synthesized with 2-butanone thiosemicarbazone. All the synthesized Fe complexes were characterized using various spectroscopic techniques and tested for their potential anticancer activity in vitro against human breast carcinoma cell line MDA-MB 231 and human lung carcinoma cell line A549 cell line using MTT assay. [FeL(2-pic)2], [FeL(bpy)], and [FeL(py)2] were found to exhibit significant antiproliferative activity with IC50 values in the range of 80-100 µM against breast and lung cancer cells. The synthesized Fe complexes also displayed mild antioxidant activities. The synthesized and studied Fe complexes have the potential for development into future anticancer agents if analyzed and modified further for improvement of their ADMET, solubility and permeability criteria set for potential drug-candidates.

Synthesis, characterization, computational studies and biological activity evaluation of Cu, Fe, Co and Zn complexes with 2-butanone thiosemicarbazone and 1,10-phenanthroline ligands as anticancer and antibacterial agents.

Mixed-ligand metal (II) (M=Cu, Fe, Co and Zn) complexes containing 2-butanone thiosemicarbazone and 1, 10-phenanthroline have been synthesized and characterized by melting point, FT-IR, 1H-NMR, UV-spectrophotometry and molar conductance measurements. All the complexes were soluble in DMSO and DMF. They were thermally stable with high melting points. The computational studies of the complexes were also performed to assess toxicity potential, bioactivity score prediction and drug likeliness assessment based on various drug filters. All the complexes showed no Veber's violations whereas only Cu complex showed one Lipinski's violation. Almost all synthesized compounds were predicted to have no toxic effects. Some of them showed positive bioactivity as enzyme inhibitors. Molecular docking of the complexes was also performed against ribonucleotide diphosphate reductase (RR) and topoisomerase II (Topo II) for minimum binding energy (kcal/mol) calculations. Cu complex was found to have minimum binding energy (-101.13 kcal/mol) released on interaction with Topo II showing a high affinity towards the enzyme, whereas Fe complex had the lowest binding energy (-99.8349 kcal/mol) when docked with RR. The results were compared with two standard drugs i.e. doxorubicin HCl and tetracycline. The ligand was tested for its potential anticancer activity against MDA-MB-231 cell line using MTT assay. Antibacterial activity of the complexes was tested against Staphylococcus aureus and Escherichia coli using the disc diffusion method. Cu (II) complex showed maximum activity against the MDA cells and also exhibited mild antibacterial activity against S. aureus.

Molecular docking, PASS analysis, bioactivity score prediction, synthesis, characterization and biological activity evaluation of a functionalized 2-butanone thiosemicarbazone ligand and its complexes.

2-Butanone thiosemicarbazone ligand was prepared by condensation reaction between thiosemicarbazide and butanone. The ligand was characterized by 1H NMR, 13C NMR, FT-IR, mass spectrometry and UV spectroscopic studies. Docking studies were performed to study inhibitory action against topoisomerase II (Topo II) and ribonucleoside diphosphate reductase (RR) enzymes. Inhibition constants (Ki ) of the ligand were 437.87 and 327.4 µM for the two enzymes, respectively. The ligand was tested for its potential anticancer activity against two cancer cell lines MDA-MB-231 and A549 using MTT assay and was found to exhibit good activity at higher doses with an IC50 = 80 µM against human breast cancer cell line MDA-MB-231. On the other hand, no significant activity was obtained against the lung carcinoma cell line A549. Antibacterial activity of the ligand was tested against Staphylococcus aureus and E. coli using the disc diffusion method. Ligand did not exhibit any significant antibacterial activity. Four complexes of Co(III), Fe(II), Cu(II), and Zn(II) were prepared with the ligand and characterized by various spectroscopic studies. Low molar conductance values were obtained for all complexes displaying non-electrolyte nature except in Co(III) complex. As expected, complexation with metal ions significantly increased the cytotoxicity of the ligand against the tested cell lines viz. IC50 values of <20 µM for Co, Fe, and Zn complexes and approx. 80 µM against MDA cells versus IC50 value of <20 µM for Co and Cu complexes and that of 30 and 50 µM for Fe and Zn complexes, respectively, against A549 cells. The Cu complex was found to be active against E. coli and S. aureus with MIC values in the range of 6-10 mg/mL. Other than Cu, only Co complex was found to possess antibacterial activity with MIC values of 5-10 mg/mL when tested against S. aureus. Bioactivity score and Prediction of Activity Spectra for Substances (PASS) analysis also depicted the drug-like nature of ligand and complexes.

Thiazolidin-4-one and thiazinan-4-one derivatives analogous to rosiglitazone as potential antihyperglycemic and antidyslipidemic agents.

A number of thiazolidin-4-one and thiazinan-4-one derivatives were prepared by three component condensation in one pot reaction method. These compounds were evaluated for anti-hyperglycemic activity by in vitro and in vivo assay systems. The compounds with thiazolidin-4-one and thiazinan-4-one moieties exhibited significant anti-hyperglycemic activity. A few compounds (3a, 3b, 4a and 4b) have exhibited both anti-hyperglycemic and anti-dyslipidemic activities. Among them the thiazinan-4-one derivative 4a showed maximal (45%) improvement in oral glucose tolerance test in db/db mice at 30 mg/kg oral dose.

Anti-stroke profile of thiazolidin-4-one derivatives in focal cerebral ischemia model in rat.

Recently, some PPARγ agonists like pioglitazone, rosiglitazone, and other newer thiazolidine-2, 4-dione (TZD) derivatives have been shown to be neuroprotective in experimental model of cerebral ischemia/reperfusion (I/R) injury. Replacement of active pharmacophore viz: thiazolidine-2,4-dione of these PPARγ agonists with biologically privileged scaffold thiazolidin-4-one derivatives have been synthesized and bioevaluated in focal cerebral ischemia model in rats with an aim to ameliorate cerebral ischemic damage. Of 20 synthesized molecules, three of the substituted compounds (2, 6 and 18) have shown significant (p < 0.001) neuroprotection even much better than rosiglitazone at same dose, when administered 1 h prior to 2/24hrI/R cerebral injury in rats, whereas compounds 10, 15, and 17 also showed significant but moderate effect on most of the parameters used in the study. Moreover, compound 2 and 6 also showed curative potential after 6 h post I/R treatment. The compound 2 has also shown significant effect on glutamate uptake by perhaps enhancing the GLT-1 activity. Thus, the present study indicates that some of the synthesized thiazolidin-4-one substituted PPARγ agonists exhibit better neuroprotection and have potential to ameliorate the ischemic damage. Therefore, this novel class of compounds could be further suitably modified to obtain potent anti-ischemic agents, warranting clinical exploitation.