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Qikprop

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QikProp is a computational tool developed by Schrödinger that predicts important physicochemical properties of drug-like molecules. It uses a knowledge-based approach to provide rapid and reliable estimates of various molecular properties, including solubility, permeability, and metabolic stability, which are crucial factors in drug development.

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Lab products found in correlation

Maestro, by Schrödinger (12 mentions) Ligprep, by Schrödinger (10 mentions) Maestro 10, by Schrödinger (3 mentions) Schrodinger suite, by Schrödinger (2 mentions) Suite 2019, by Schrödinger (2 mentions) Ligprep module, by Schrödinger (2 mentions) Molecular modeling suite, by Schrödinger (2 mentions) Qikprop software, by Schrödinger (1 mentions) Qikprop v 6, by Schrödinger (1 mentions) Software suite, by Schrödinger (1 mentions) Maestro 12, by Schrödinger (1 mentions) Accelrys discovery studio visualizer 3, by Dassault Systèmes (1 mentions) Marvinsketch 5, by ChemAxon (1 mentions) Chemdraw, by PerkinElmer (1 mentions) Qikprop3, by Schrödinger (1 mentions) Matlab neural network toolbox, by MathWorks (1 mentions) Jaguar, by Schrödinger (1 mentions) Maestro 11, by Schrödinger (1 mentions) Protein preparation wizard, by Schrödinger (1 mentions) Qikprop version 4, by Schrödinger (1 mentions)

143 protocols using qikprop

1

Pharmacokinetic Characteristics of PQ2

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Some pharmacokinetic characteristics of PQ2 were calculated by the QikProp module of Schrödinger software (Schrödinger Release 2016-2: QikProp, Schrödinger, LLC, New York, NY, USA, 2016) [47 (link),48 (link)].
Ciftci H., Sever B., Ocak F., Bayrak N., Yıldız M., Yıldırım H., DeMirci H., Tateishi H., Otsuka M., Fujita M, & TuYuN A.F. (2022). In Vitro and In Silico Study of Analogs of Plant Product Plastoquinone to Be Effective in Colorectal Cancer Treatment. Molecules, 27(3), 693.
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2

Compound Characterization and Antiviral Evaluation

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Compound properties are reported in Tables 1–4. Structures were optimized using LigPrep (LigPrep, Schrodinger, LLC, New York, NY, 2018). Pharmaceutically relevant properties including logP (water / octanol partition coefficient) and logS (aqueous solubility) were calculated using QikProp (QikProp, Schrodinger, LLC, New York, NY, 2018). Inhibition constants for HP-binding (KI) were measured in a competitive inhibition fluorescence experiment[23 (link)] by concentration-dependent displacement of fluorescently labeled HP-binding C- peptide from the NHR binding site. Concentrations that yielded 50% inhibition of biological activity (IC50) were obtained using cell-cell fusion (IC50CCF) and viral infectivity (virus-cell fusion; IC50VCF) assays as previously described.[2 (link)] Antiviral assays were run using lab-adapted viral strains Ba-L and IIIB. Details are in the Supplementary Data.
Zhou G., Chu S., Nemati A., Huang C., Snyder B.A., Ptak R.G, & Gochin M. (2018). Investigation of the molecular characteristics of bisindole inhibitors as HIV-1 glycoprotein-41 fusion inhibitors. European journal of medicinal chemistry, 161, 533-542.
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3

Computational ADME Profiling of Synthesized Compounds

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Two computational tools were utilized to predict the absorption, distribution, metabolism, and excretion (ADME) of the synthesized compounds, SWISSADME (http://www.swissadme.ch/) (accessed on 14 November 2021) [57 (link)] and QikProp (QikProp, Schrödinger, LLC, New York, NY, 2021). The important pharmaceutical properties that were selected for evaluation were gastrointestinal (GI) absorption, blood–brain barrier (BBB) permeability, P-glycoprotein (P-gp) substrate, lipophilicity (log Po/w), and solubility (Log S).
Suliman R.S., Alghamdi S.S., Ali R., Rahman I., Alqahtani T., Frah I.K., Aljatli D.A., Huwaizi S., Algheribe S., Alehaideb Z, & Islam I. (2022). Distinct Mechanisms of Cytotoxicity in Novel Nitrogenous Heterocycles: Future Directions for a New Anti-Cancer Agent. Molecules, 27(8), 2409.
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4

Predicting Pharmacokinetic Properties of L-HIPPO

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Some crucial pharmacokinetic properties of the new L-HIPPO derivatives were predicted by the QikProp module in Maestro (QikProp, Schrödinger, LLC, NY, 2016).
Ciftci H., Sever B., Ayan E., Can M., DeMirci H., Otsuka M., TuYuN A.F., Tateishi H, & Fujita M. (2022). Identification of New L-Heptanoylphosphatidyl Inositol Pentakisphosphate Derivatives Targeting the Interaction with HIV-1 Gag by Molecular Modelling Studies. Pharmaceuticals, 15(10), 1255.
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5

ADME Properties of Isolated Compounds

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The selected ligands (isolated compounds) were checked for their ADME properties using QikProp (QikProp, Schrödinger, LLC, New York, NY, 2017). The pharmacokinetics and pharmacodynamics were calculated using the properties of drugs.
Palanisamy C.P., Cui B., Zhang H., Jayaraman S., Rajagopal P, & Veeraraghavan V.P. (2022). (5E,7E)-4,5,6 Trihydroxy-3-(hydroxymethyl)tetrahydro-2H-pyran-2-ylheptadeca-5,7-dienoate from Euclea crispa (L.) Inhibits Ovarian Cancer Cell Growth by Controlling Apoptotic and Metastatic Signaling Mechanisms. Bioinorganic Chemistry and Applications, 2022, 4464056.
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6

In silico ADME Profiling of Flavonoids

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Drug molecules with favorable absorption, distribution, metabolism, and elimination (ADME) properties are the primary indicators of successful candidate molecules in drug discovery and development. In this study, QikProp filter from Schrödinger was used to calculate several pharmacokinetic and pharmacodynamic properties of Oroxylin A, Baicalein and Chrysin. The QikProp set of descriptors (SASA, FOSA, FISA, PISA, #metabolites, CNS distribution, QPlog BB, Donor HB, Accept HB, logP, % human oral absorption, and Rule of 5) were selected to describe this aspect of the compounds permeability, metabolism and activity. Schrödinger Release 2019–2: QikProp, Schrödinger, LLC, New York, NY was used in the computational analysis.
Pondugula S.R., Majrashi M., Almaghrabi M., Ramesh S., Abbott K.L., Govindarajulu M., Gill K., Fahoury E., Narayanan N., Desai D., Ren J., Nadar R., McElroy T., Moore T., Majeed M., Kalyanam N, & Dhanasekaran M. (2021). Oroxylum Indicum ameliorates chemotherapy induced cognitive impairment. PLoS ONE, 16(6), e0252522.
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7

Predicting ADME and Toxicity of MraY Inhibitors

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The predicted absorption, distribution, metabolism, and excretion (ADME) properties of the potential MraYMtb inhibitors were calculated using the QikProp module (QikProp, version 12.3.013, Schrödinger, LLC, New York, NY, 2020) implemented in the Schrödinger software. The important toxicity parameters were calculated using admetSAR version 2.0.50 (link) The QikProp module predicts pharmaceutically relevant properties of the given molecules, and also provides the recommended values for the properties based on the analysis of 95% of marketed drugs used in their training set. These recommended values are used for the comparison. The potential hits were preprocessed using LigPrep. The QikProp calculation was run in normal mode. In addition, the toxicity profile was calculated using an online server of admetSAR software, with SMILES notation as input.
Pandey P., Chatterjee S., Berida T., Doerksen R.J, & Roy S. (2020). Identification of Potential Non-nucleoside MraY Inhibitors for Tuberculosis Chemotherapy Using Structure-Based Virtual Screening. Journal of biomolecular structure & dynamics, 40(11), 4832-4849.
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8

Evaluating ADME Properties of Phytochemicals

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Drug molecules with favorable absorption, distribution, metabolism, and elimination (ADME) properties have been identified as the primary indicators of successful candidate molecules in drug discovery and development. In this study, QikProp filter from Schrödinger was used to calculate several pharmacokinetic and pharmacodynamic properties of piperine, AKBA, and KBA. The QikProp set of descriptors (SASA, FOSA, FISA, PISA, #metabolites, CNS distribution, QPlog BB, Donor HB, Accept HB, logP, % human oral absorption, and Rule of 5) were selected to describe permeability, metabolism and activity. Schrödinger release 2020: QikProp, Schrödinger, LLC, New York, NY software was used in the computational analysis.
Vijayarani K.R., Govindarajulu M., Ramesh S., Alturki M., Majrashi M., Fujihashi A., Almaghrabi M., Kirubakaran N., Ren J., Babu R.J., Smith F., Moore T, & Dhanasekaran M. (2020). Enhanced Bioavailability of Boswellic Acid by Piper longum: A Computational and Pharmacokinetic Study. Frontiers in Pharmacology, 11, 551911.
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9

In silico Pharmacokinetic Profiling

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In silico pharmacokinetic profiles of compounds 1–7 were determined using the QikProp module of Schrödinger software (Schrödinger Release 2016-2: QikProp, Schrödinger, LLC, New York, NY, USA).
Özdemir A., Ciftci H., Sever B., Tateishi H., Otsuka M., Fujita M, & Altıntop M.D. (2022). A New Series of Indeno[1,2-c]pyrazoles as EGFR TK Inhibitors for NSCLC Therapy. Molecules, 27(2), 485.
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10

Pharmacokinetic Analysis of Fucosterol

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Pharmacokinetic parameters including absorption, distribution, metabolism, and excretion/transport (ADME/T) of fucosterol were analyzed through QikProp (Schrödinger Release 2019-3: QikProp, Schrödinger, LLC, New York, NY, USA). QikProp is an efficient ADME/T prediction tool that forecasts whether the selected compound would exhibit satisfactory ADME/T performances during clinical trials.
Hannan M.A., Dash R., Sohag A.A, & Moon I.S. (2019). Deciphering Molecular Mechanism of the Neuropharmacological Action of Fucosterol through Integrated System Pharmacology and In Silico Analysis. Marine Drugs, 17(11), 0.
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