PASS: prediction of activity spectra for biologically active
  substances

Lagunin, Alexey; Stepanchikova, A. V.; Филимонов, Д. А.; Poroikov, Vladimir

doi:10.1093/bioinformatics/16.8.747

Cited by 849 publications

(494 citation statements)

References 1 publication

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“…The structure of ethambutol was also retrieved from Drug Bank. Structural similarity, sub-structure, identity (70%) search were performed and carried out for ethambutol like compounds using Molsoft ICM Browser 3.5-1p and ChemBioDraw Ultra 12.0 software (Gogoi, et al, 2012;Lagunin, et al, 2000). Compounds library were collected from ZINC Database, PubChem, Chemspider, ChemBank cheminformatics site in sdf format.…”

Section: Methodsmentioning

confidence: 99%

Arabinosyl transferase inhibitor design against <i>Mycobacterium tuberculosis</i> using ligand based drug design approach

Kolita

Gogoi

Dutta

et al. 2014

Bangladesh J Pharmacol

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Antibiotic resistance is a major challenge to combat tuberculosis. Several reports of antibiotic resistance strains of Mycobacterium tuberculosis is strongly demanding the need of new and alternative antibiotics for its inhibition. Therefore, current investigation is an attempt to screen few lead molecules for the inhibition of arbinosyl transferase enzyme of M. tuberculosis. The inhibition of this enzyme is an established target of many antibiotics especially ethambutol. Herein, we have considered the structure of ethambutol as a starting point to screen active compound then ethambutol. Similar compounds were searched in chemical database and six compounds were identified and considered as selective arbinosyl transferase inhibitor based on physiochemical properties, bioactivity and ADME with least docking score. The compounds viz. ZINC00388344, ZINC003884, Chemspider2057082, ZINC-00388344, ZINC0038846, Chemspider2057082, Etha17 (analog) and Etha10 (analog) were finally screened and recommended for in vitro investigation. Article Info

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Section: Methodsmentioning

confidence: 99%

Arabinosyl transferase inhibitor design against <i>Mycobacterium tuberculosis</i> using ligand based drug design approach

Kolita

Gogoi

Dutta

et al. 2014

Bangladesh J Pharmacol

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“…Here, prediction of activity spectra for substances (PASS), an online software tool that predicts more than 300 pharmacological effects and biochemical mechanisms of compounds based on their structural information [45], was used to screen the possible therapeutic targets for the herbal derivatives. PASS (Prediction of activity spectra for substances) software, predicted the probability of activity (Pa) and inactivity (Pi) values for each herbal derivatives to identify the possible inhibitory targets.…”

Section: Therapeutic Target Validationmentioning

confidence: 99%

Molecular Docking and Pharmacokinetic Prediction of Herbal Derivatives as Maltase-Glucoamylase Inhibitor

Ochieng

Sumaryada

Okun

2017

Asian J Pharm Clin Res

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Objective: To perform molecular docking and pharmacokinetic prediction of momordicoside F2, beta-sitosterol, and cis-N-feruloyltyramine herbal derivatives as maltase-glucoamylase (MGAM) inhibitors for the treatment of diabetes. Methods:The herbal derivatives and standard drug miglitol were docked differently onto MGAM receptor using AutoDock Vina software. In addition, Lipinski's rule, drug-likeness, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties were analyzed using Molinspiration, ADMET structure-activity relationship, and prediction of activity spectra for substances online tools.Results: Docking studies reveal that momordicoside F2, beta-sitosterol, and cis-N-feruloyltyramine derivatives have high binding affinity to the MGAM receptor (−7.8, −6.8, and −6.5 Kcal/Mol, respectively) as compared to standard drug miglitol (−5.3 Kcal/Mol). In addition, all the herbal derivatives indicate good bioavailability (topological polar surface area <140 Ȧ and N rot <10) without toxicity or mutagenic effects. Conclusion:The molecular docking and pharmacokinetic information of herbal derivatives obtained in this study can be utilized to develop novel MGAM inhibitors having antidiabetic potential with better pharmacokinetic and pharmacodynamics profile.

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“…1 Grindstone chemistry pathway for DHPM synthesis specific biological targets. The online version of PASS program was applied for selecting the compounds with desirable and without toxicity of biological activities among the 250, 000 compounds from NCI database [23,24]. The NCI database includes drugs, drug candidates, leads, and toxic substances.…”

Section: Biological Activity Spectrum By Pass-predictionmentioning

confidence: 99%

Synthesis, antibacterial studies, and molecular modeling studies of 3,4-dihydropyrimidinone compounds

Ramachandran

Arumugasamy²,

Edayadulla

et al. 2015

J Chem Biol

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The syntheses of dihydropyrimidinones (DHPMs) using solvent-free grindstone chemistry method. All the synthesized compounds exhibited significant activity against pathogenic bacteria. The current effort has been developed to obtain new DHPM derivatives that focus on the bacterial ribosomal A site RNA as a drug target. Molecular docking simulation analysis was applied to confirm the target specificity of DHPMs. The crystal structure of bacterial 16S rRNA and human 40S rRNA was taken as receptors for docking. Finally, the docking score, binding site interaction analysis revealed that DHPMs exhibit more specificity towards 16S rRNA than known antibiotic amikacin. Accordingly, targeting the bacterial ribosomal A site RNA with potential drug leads promises to overcome the bacterial drug resistance. Even though, anti-neoplastic activities of DHPMs were also predicted through prediction of activity spectra for substances (PASS) tool. Further, the results establish that the DHPMs can serve as perfect leads against bacterial drug resistance.

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PASS: prediction of activity spectra for biologically active substances

Cited by 849 publications

References 1 publication

Arabinosyl transferase inhibitor design against <i>Mycobacterium tuberculosis</i> using ligand based drug design approach

Arabinosyl transferase inhibitor design against <i>Mycobacterium tuberculosis</i> using ligand based drug design approach

Molecular Docking and Pharmacokinetic Prediction of Herbal Derivatives as Maltase-Glucoamylase Inhibitor

Synthesis, antibacterial studies, and molecular modeling studies of 3,4-dihydropyrimidinone compounds

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