Prepwizard

Manufactured by Schrödinger

Sourced in United States

PrepWizard is a lab equipment product designed for sample preparation. It automates and streamlines the process of preparing samples for analysis. The core function of PrepWizard is to assist researchers and scientists in efficiently preparing samples for various experimental and testing purposes.

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Lab products found in correlation

Ligprep, by Schrödinger (6 mentions) Glide sp, by Schrödinger (3 mentions) Glide htvs, by Schrödinger (2 mentions) Maestro 12, by Schrödinger (2 mentions) Protein preparation wizard, by Schrödinger (1 mentions) Maestro v12, by Schrödinger (1 mentions) Glide software, by Schrödinger (1 mentions) Discovery studio 2, by Dassault Systèmes (1 mentions) Chemsketch, by Advanced Chemistry Development (1 mentions) Macromodel, by Schrödinger (1 mentions) Icm pro, by Molsoft (1 mentions)

13 protocols using prepwizard

Protein Structure Preparation for Screening

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The 3-dimensional structures of selected proteins RdRp (PDB ID: 6M71) and Mpro (PDB ID: 6Y2E) were downloaded from RCSB Protein Data Bank [52] . The structural correctness in terms of hydrogen consistency, bond orders, steric interactions, charges, optimization, energy minimization using OPLS3e forcefield were performed using protein preparation wizard (PrepWizard) of Schrodinger suite (Maestro 12.5) [53] . The minimized proteins were used for pharmacophore screening, sitemap analysis, receptor grid generation and as well as for molecular docking.

Gajjar N.D., Dhameliya T.M, & Shah G.B. (2021). In search of RdRp and Mpro inhibitors against SARS CoV-2: Molecular docking, molecular dynamic simulations and ADMET analysis. Journal of Molecular Structure, 1239, 130488.

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Preparing Structural Files of Human MAO-A

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Protein structural files of the human MAO-A were acquired from the Protein Data Bank (PDB codes: 2BXR (De Colibus et al., 2005 (link)), 2BXS (De Colibus et al., 2005 (link)), 2Z5X (Son et al., 2008 ), 2Z5Y (Son et al., 2008 )). The protein structures were prepared by operating the Protein Preparation Wizard (Sastry et al., 2013 (link)) (PrepWizard) of Schrödinger suite to assign bond orders, to add all missing hydrogen atoms, and to fill in missing side chains and loops with Prime (Jacobson et al., 2002 (link); Jacobson et al., 2004 ). Those water molecules that are located within 5 Å from the native ligand and are forming at least two hydrogen bonds with non-waters were retained. The hydrogen bonding network was assigned and optimized by considering possible water orientations, minimizing the hydrogens of altered species and by sampling the flips for Asn, Gln, and His. The protein-ligand complexes were relaxed with Impref using OPLS2005 force field.

Larit F., Elokely K.M., Chaurasiya N.D., Benyahia S., Nael M.A., León F., Abu-Darwish M.S., Efferth T., Wang Y.H., Belouahem-Abed D., Benayache S., Tekwani B.L, & Cutler S.J. (2017). Inhibition of human monoamine oxidase A and B by flavonoids isolated from two Algerian medicinal plants. Phytomedicine : international journal of phytotherapy and phytopharmacology, 40, 27-36.

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High-Throughput Screening of ZMYND11 PWWP Binders

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The X-ray structure of the PWWP domain of ZMYND11 (PDB ID: 4N4I)^{14 (link)} was prepared with PrepWizard (Schrodinger, New York) using the standard protocol, including the addition of hydrogens, the assignment of bond order, assessment of the correct protonation states, and a restrained minimization using the OPLS-AA 2005 force field. Receptor grids were calculated at the centroid of the trimethyllysine (M3L) with the option to dock ligands of similar size.
A lead-like library of ~2 million compounds was prepared with LigPrep (Schrodinger, New York). The resulting library was then docked using the virtual screening workflow using Glide HTVS in the first stage, followed by Glide SP in the second stage (Schrodinger, New York). After removing the compounds with a docking score worse than −7 kcal/mol and that do not contain a tertiary amine, the remaining 18k compounds were docked with Glide XP. Next, compounds with a docking score better than −8 kcal/mol or with a score better than −6 kcal/mol and two hydrogen bonds with nearby residues (R317, F311, H313, N316, W319, H314, S340) were selected for visual inspection. This step selected 431 compounds, which were rescored with the GBSA method (AMBER 12, UCSF). The compounds were clustered and the ones with GBSA > −15 kcal/mol were removed. Finally, after a visual inspection, 40 compounds were selected to be purchased.

de Freitas R.F., Liu Y., Szewczyk M.M., Mehta N., Li F., McLeod D., Zepeda-Velázquez C., Dilworth D., Hanley R.P., Gibson E., Brown P.J., Al-Awar R., James L.I., Arrowsmith C.H., Barsyte-Lovejoy D., Min J., Vedadi M., Schapira M, & Allali-Hassani A. (2021). Discovery of Small-Molecule Antagonists of the PWWP Domain of NSD2. Journal of medicinal chemistry, 64(3), 1584-1592.

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Structural Preparation of Human MCM7 Protein

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The crystal structure of human MCM7 protein (PDB code: 6XTY) was downloaded from RCSB Protein Data Bank (PDB)^{47 (link)}. MCM7 protein was co-crystalized with the MCM protein family, therefore the target MCM7 protein was separated and removed the water, metal ions, cofactors, other molecules, and other proteins by the Maestro v-12.5 of Schrödinger Suite 2020-3⁴⁸. The MCM7 protein was initially processed and prepared by the protein preparation wizard (Prep Wizard) of Schrödinger Suite 2020-3^{49 (link)}. The prepared protein has been further utilized for molecular docking and other experiments.

Samad A., Huq M.A, & Rahman M.S. (2022). Bioinformatics approaches identified dasatinib and bortezomib inhibit the activity of MCM7 protein as a potential treatment against human cancer. Scientific Reports, 12, 1539.

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Structural Determination and Ligand Docking of Tubulin

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The 3D crystal structure of Tubulin (PDB: 4O2B) was obtained from the RCSB protein data bank, and the structure was prepared using the Protein Preparation Wizard tool (PrepWizard, Schrödinger Release 2021-1). The 3D Tubulin structure was refined, minimized, and optimized with the OPLS4 force field. Unnecessary water molecules, substrates, ions, and other subunits were removed and the β-Tubulin subunit that contains the Colchicine binding site was maintained for the docking study. The 2D structures for ligands (F1-11, S1-3, D1-4, and Colchicine) were prepared using Schrödinger’s LigPrep tool, and several conformations were generated, optimized, and minimized for their lowest energy conformation.

Alghamdi S.S., Suliman R.S., Alsaeed A.S., Almutairi K.K., Aljammaz N.A., Altolayyan A., Ali R, & Alhallaj A. (2021). Novel Anti-Tubulin Compounds from Trigonella foenum-graecum Seeds; Insights into In-vitro and Molecular Docking Studies. Drug Design, Development and Therapy, 15, 4195-4211.

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Structural Insights into XIAP-BIR3 Complex

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During this study, X-ray structures of the following complexes with XIAP-BIR3 retrieved from the PDB database were used (Table 4): 5C7C [20 (link)], 5M6M [21 (link)], 5OQW [22 (link)] and 5M6L [21 (link)]. Then, to calculate the experimental value of ligand binding free energy

∆ G_{e x p}

, the following equation was applied:

∆ G_{e x p} = R T \times \ln {I C}_{50}

where the gas constant value was R = 1.985 8775 × 10⁻³ kcal·K⁻¹·mol⁻¹ and T = 303, 15 K.
As the XIAP-BIR3 complex with Smac AVPI tetra peptide was not solved to date, to prepare this complex, we chose to apply the docking strategy. The AVPI tetra peptide, which was retrieved from the PDB structure of XIAP-BIR3 co-crystallized with full SMAC (PDB ID: 1G73 [12 (link)]), was docked into the X-ray crystal structure 5C7C of XIAP-BIR3, without waters and bounded synthetic ligand. The docking was carried out using Glide software (Schrödinger^®) with the default parameters [31 ]. The protein structure was prepared before using Schrödinger Protein Preparation Wizard (PrepWizard) [31 ]. The Glide score was used to evaluate the generated AVPI poses, and the pose with the best score was selected as a starting structure for MD simulations.

Farag M., Kieffer C., Guedeney N., Voisin-Chiret A.S, & Sopkova-de Oliveira Santos J. (2023). Computational Tool to Design Small Synthetic Inhibitors Selective for XIAP-BIR3 Domain. Molecules, 28(13), 5155.

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Optimizing NSD2 PWWP Domain Inhibitors

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The X-ray structure of the PWWP domain of NSD2 in complex with MR837 (PDB: 6UE6) was prepared with PrepWizard (Schrodinger) using the standard protocol, including the addition of hydrogens, the assignment of bond order, the assessment of the correct protonation states and a restrained minimization using the OPLS3 force field. Receptor grids were calculated at the centroid of the ligand with the option to dock ligands of similar size, and a hydrogen-bonding constraint with the backbone of A270 was defined. Over 6,000 commercially available chemical analogs of MR837 were prepared with LigPrep (Schrodinger). The resulting library was then docked using Glide SP (Schrodinger) with default settings. Also, the core docking option was turned on to allow only ligand poses that had their core aligned within 1.0 Å of the reference core (the cyclopropyl and the amide group of MR837). Only 448 compounds fitted and were ranked by Glide. Finally, after a visual inspection, 20 compounds were ordered. Optimization and structure–activity relationship (SAR) leading from MRT866 to UNC6934 was guided by free energy perturbation and will be presented elsewhere.

Dilworth D., Hanley R.P., de Freitas R.F., Allali-Hassani A., Zhou M., Mehta N., Marunde M.R., Ackloo S., Machado R.A., Yazdi A.K., Owens D.D., Vu V., Nie D.Y., Alqazzaz M., Marcon E., Li F., Chau I., Bolotokova A., Qin S., Lei M., Liu Y., Szewczyk M.M., Dong A., Kazemzadeh S., Abramyan T., Popova I.K., Hall N.W., Meiners M.J., Cheek M.A., Gibson E., Kireev D., Greenblatt J.F., Keogh M.C., Min J., Brown P.J., Vedadi M., Arrowsmith C.H., Barsyte-Lovejoy D., James L.I, & Schapira M. (2021). A chemical probe targeting the PWWP domain alters NSD2 nucleolar localization. Nature chemical biology, 18(1), 56-63.

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KSHV Protease Structure Optimization and Virtual Screening

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PDB ID 4P3H was used to represent KSHV-encoded protease ORF17. Discovery studio 2.5 (DS, Accelrys Inc., San Diego) was used to remove all the water molecule except from the catalytic region. Addition of hydrogen atoms and optimization of side chain was performed using Prepwizard (Schrodinger suite). Prediction of Ionizable groups at neutral pH was performed by PROPKA. H-bond optimization was performed by ProtAssign. Impref utility module was used for structure minimization allowing restrain on heavy atoms only. The centroid of ligand N-[2-Benzyl-4-(1 h-Tetrazol-5-Yl) phenyl]-6-(Cyclohexylmethyl) pyridine-2-Carboxamide is used as the grid center. Chemical compounds of biological origin were downloaded from ZINC database. A library of 307,814 compounds of biological origin has been used as a screen library. Based on ionization states (ionization states possible between pH 5–9) and specified chirality (possible stereoisomer for specified carbon), the number of total compounds were 481,799. The list of top 10 ligands after the virtual screening is provided in Table 1.

Rafeeq M.M., Habib A.H., Nahhas A.F., Binothman N., Aljadani M., Almulhim J., Sain Z.M., Alam M.Z., Alturki N.A., Alam Q., Manish M, & Singh R.K. (2023). Targeting Kaposi’s sarcoma associated herpesvirus encoded protease (ORF17) by a lysophosphatidic acid molecule for treating KSHV associated diseases. Frontiers in Cell and Developmental Biology, 11, 1060156.

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Docking Analysis of GS-CA1 and Coumermycin A1 on HIV-1 Capsid

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The X-ray crystal structure of native HIV-1 capsid protein bound to PF74 (PDB entry 4XFZ) (Gres et al., 2015 (link)) was used to dock GS-CA1 and Coumermycin A1 (C-A1). Initial structures of GS-CA1 and C-A1 were generated with ChemSketch (Advanced Chemistry Development, Inc., Toronto, Ontario, Canada). These structures were subsequently minimized using MacroModel followed by LigPrep (Schrödinger Inc. NY). The PrepWizard (Schrödinger Inc. NY), which adds hydrogens, assigns bond orders, creates heteroatom states, and samples conformations of water molecules, was used to prepare CA-hexamer for docking of GS-CA1 and C-A1.

Singh K., Gallazzi F., Hill K.J., Burke D.H., Lange M.J., Quinn T.P., Neogi U, & Sönnerborg A. (2019). GS-CA Compounds: First-In-Class HIV-1 Capsid Inhibitors Covering Multiple Grounds. Frontiers in Microbiology, 10, 1227.

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Protein Structure Preparation for Analysis

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The first step in protein processing was to extract the desired protein structure from the AlphaFold2. Subsequently, the Protein Preparation Wizard (PrepWizard), part of the Schrödinger suite (Maestro 12.8) [53 ], was used to perform several preprocessing steps on the protein structure. These steps involved the addition of missing hydrogen atoms, side-chain optimization, the correction of the ionization state of the protein, and the assignment of bond orders and formal charges. In addition, advanced algorithms were used to refine the protein structures. For example, they were used in the removal of water molecules and in energy minimization using the Optimized Potentials for Liquid Simulation 4 (OPLS4) force field.

Zia S., Sumon M.M., Ashik M.A., Basar A., Lim S., Oh Y., Park Y, & Rahman M.M. (2024). Potential Inhibitors of Lumpy Skin Disease’s Viral Protein (DNA Polymerase): A Combination of Bioinformatics Approaches. Animals : an Open Access Journal from MDPI, 14(9), 1283.

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