Log In Sign up
The largest database of trusted experimental protocols

Small molecule drug discovery suite

Manufactured by Schrödinger
Visit Supplier
Sourced in United States

The Small-Molecule Drug Discovery Suite is a comprehensive software platform designed for the in silico exploration and development of small-molecule compounds. The suite provides a range of computational tools and algorithms to support various stages of the drug discovery process, including molecular modeling, virtual screening, and lead optimization.

Automatically generated - may contain errors

Lab products found in correlation

Protein preparation wizard, by Schrödinger (7 mentions) Maestro, by Schrödinger (6 mentions) Ligprep, by Schrödinger (2 mentions) Ligprep tool, by Schrödinger (2 mentions) Sitemap, by Schrödinger (1 mentions) Instant jchem, by ChemAxon (1 mentions) Glide program, by Schrödinger (1 mentions) Chemdraw, by PerkinElmer (1 mentions) Biovia discovery studio, by Dassault Systèmes (1 mentions) Ligand preparation wizard, by Schrödinger (1 mentions) Prime module, by Schrödinger (1 mentions) Pymol molecular graphics system, by Schrödinger (1 mentions) Qikprop, by Schrödinger (1 mentions)

40 protocols using small molecule drug discovery suite

1

Molecular Docking of GPR52 Inhibitor

Check if the same lab product or an alternative is used in the 5 most similar protocols
The molecular docking study was performed using Schrödinger Small-Molecule Drug Discovery Suite (Schrödinger, LLC, New York, NY, 2020). The cocrystal structures of GPR52 and compound 2 (PDB code: 6LI0) were downloaded from the RCS PDB bank. The cocrystal structure was preprocessed and minimized with Schrödinger Protein Preparation Wizard using default settings. The grid center was chosen on the centroid of an existing ligand, and the size of the grid box was set to 30 Å on each side. The 3D structure of ligand 12c was created using Schrödinger Maestro, and a low energy conformation was calculated using LigPrep. Docking was employed with Glide using the SP precision. Docked poses were incorporated into Schrödinger Maestro for visualization and analysis of binding site interactions.
Wang P., Felsing D.E., Chen H., Stutz S.J., Murphy R.E., Cunningham K.A., Allen J.A, & Zhou J. (2020). Discovery of Potent and Brain-Penetrant GPR52 Agonist that Suppresses Psychostimulant Behavior. Journal of medicinal chemistry, 63(22), 13951-13972.
+ Open protocol
+ Expand
2

Molecular Docking Study of Compound 38

Check if the same lab product or an alternative is used in the 5 most similar protocols
The molecular docking study was performed using Schrödinger Small-Molecule Drug Discovery Suite (Schrödinger, LLC, New York, NY, 2020). Human Sirt6 in complex with an activator UBCS039 crystal structure (PDB ID: 5MF6) was downloaded from RCSB PDB bank [28 ]. The structure was prepared using Protein Preparation Wizard with default settings. During the preparation, hydrogens were added, crystal waters beyond 3 Å from existing ligand were removed, partial charges were assigned, and structure was minimized. 3D-structure of compound 38 (GL0710) was generated using Maestro and further prepared with LigPrep using OPLS3 forcefield. Compound 38 was ionized at target pH 7.4, desalted and tautomers were generated using Epik, and a low energy conformation was calculated. The grid box in size of 24 Å on each side was created with Glide. The grid center was chosen on the center of the existing ligand based on the binding site of crystal structure. Docking was employed with Glide using the SP protocol. Docked poses were incorporated into Schrödinger Maestro for a ligand-receptor interactions analysis. The final pose selected was among the best scoring poses. The selected pose was superimposed with Sirt6-UBCS039 complex structure for an overlay analysis.
Xu J., Shi S., Liu G., Xie X., Li J., Bolinger A.A., Chen H., Zhang W., Shi P.Y., Liu H, & Zhou J. (2022). Design, synthesis, and pharmacological evaluations of pyrrolo[1,2-a]quinoxaline-based derivatives as potent and selective sirt6 activators. European journal of medicinal chemistry, 246, 114998.
+ Open protocol
+ Expand
3

Molecular Docking of PW201 to FGF14:Nav1.6 Complex

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
The molecular docking study was performed using Schrödinger Small-Molecule Drug Discovery Suite (Schrödinger, LLC, New York, NY, USA). The FGF14:Nav1.6 homology model was built using the FGF13:Nav1.5:CaM ternary complex crystal structure (PDB code: 4DCK) as a template [14 (link)]. The FGF14:Nav1.6 CTD homology model was prepared with Schrödinger Protein Preparation Wizard using default settings. The SiteMap (Schrödinger, LLC) calculation was performed, and a potential binding site was identified on the PPI interface of FGF14 and the CTD of the Nav1.6 channel. The docking was performed on the CTD of Nav1.6 after removing the FGF14 chain structure. The grid center was chosen on the Nav1.6 CTD at the previously identified binding site with a grid box sized in 24 Å covering the PPI surface on the Nav1.6 CTD. The 3D structure of PW201 was created using Schrödinger Maestro and a low-energy conformation was generated using LigPrep. Docking was then employed with Glide using the SP precision. Docked poses were incorporated into Schrödinger Maestro for a ligand–receptor interactions visualization. The top docked pose of PW201 was superimposed with the FGF14:Nav1.6 CTD complex homology model for an overlay analysis.
Dvorak N.M., Tapia C.M., Singh A.K., Baumgartner T.J., Wang P., Chen H., Wadsworth P.A., Zhou J, & Laezza F. (2021). Pharmacologically Targeting the Fibroblast Growth Factor 14 Interaction Site on the Voltage-Gated Na+ Channel 1.6 Enables Isoform-Selective Modulation. International Journal of Molecular Sciences, 22(24), 13541.
+ Open protocol
+ Expand
4

Molecular Docking of FGF14:Nav1.6 Complex

Check if the same lab product or an alternative is used in the 5 most similar protocols
The molecular docking study was carried out using Schrödinger Small-Molecule Drug Discovery Suite (Schrödinger, LLC, New York, NY, 2020). FGF14:Nav1.6 homology model was generated using the FGF13:Nav1.5: CaM ternary complex crystal structure (PDB code: 4DCK) as a template. The FGF14:Nav1.6 homology model was prepared with Schrödinger Protein Preparation Wizard using default settings. During this step, hydrogens were added, crystal waters were removed, and partial charges were assigned using the OPLS-2005 force field. The SiteMap calculation was investigated and a potential binding site was identified on the PPI of FGF14:Nav1.6. The chain of Nav1.6 was excluded and the grid center was chosen on the center of this previous identified binding site with a grid box in size of 24 Å on each side. The 3D structure of ligand 21a was created using Schrödinger Maestro and a low energy conformation was calculated using LigPrep. Docking was employed with Glide using the SP protocol. Docked poses were incorporated into Schrödinger Maestro for a ligand-receptor interactions visualization. The top docked pose of 21a was selected and superimposed with FGF14:Nav1.6 complex homology model for an overlay analysis.
Wang P., Wadsworth P.A., Dvorak N.M., Singh A.K., Chen H., Liu Z., Zhou R., Holthauzen L.M., Zhou J, & Laezza F. (2020). Design, Synthesis, and Pharmacological Evaluation of Analogs Derived from the PLEV Tetrapeptide as Protein-Protein Interaction Modulators of Voltage-Gated Sodium Channel 1.6. Journal of medicinal chemistry, 63(20), 11522-11547.
+ Open protocol
+ Expand
5

Computational Drug Discovery with Schrödinger

Check if the same lab product or an alternative is used in the 5 most similar protocols
The Schrödinger Small-Molecule Drug Discovery Suite was used for performing this computational study. The computational simulation experiments were performed in Maestro, the unified graphical interface of Schrödinger. Computational methods were as per earlier reports with little modifications18 –21 (link). In this computational study, various modules were used in the Maestro, including Protein Preparation Wizard (PPW), Prime, Glide and Desmond.
Baby K., Maity S., Mehta C.H., Nayak U.Y., Shenoy G.G., Pai K.S., Harikumar K.B, & Nayak Y. (2023). Computational drug repurposing of Akt-1 allosteric inhibitors for non-small cell lung cancer. Scientific Reports, 13, 7947.
+ Open protocol
+ Expand
6

Molecular Docking of FGF14 Peptides

Check if the same lab product or an alternative is used in the 5 most similar protocols
The docking study was performed with Schrödinger Small‐Molecule Drug Discovery Suite using the FGF14 chain of a previously described FGF14:Nav1.6 homology model (Ali et al., 2016). The protein structure was prepared with Protein Prepared Wizard. FLPK, EYYV, and PLEV peptide fragments (containing N‐terminal acetylation and C‐terminal amidation) were prepared with LigPrep and the initial lowest energy conformation was calculated. The grid center was chosen on the coordinate of X = 27.4, Y = −14.88, Z = −15.97. Grid box size was set to 50 × 50 × 50 Å and a finer scaling factor of 0.5 was used. Grid generation and docking were both employed with Glide using SP‐Peptide protocol. Docking poses were incorporated into Schrödinger Maestro for a visualization of ligand‐receptor interactions. Overlay analysis was performed with the docked pose of FLPK, PLEV, EYYV and FGF14:Nav1.6 homology model using Schrödinger Maestro.
Singh A.K., Wadsworth P.A., Tapia C.M., Aceto G., Ali S.R., Chen H., D'Ascenzo M., Zhou J, & Laezza F. (2020). Mapping of the FGF14:Nav1.6 complex interface reveals FLPK as a functionally active peptide modulating excitability. Physiological Reports, 8(14), e14505.
+ Open protocol
+ Expand
7

Optimizing 5-HT7R Targeting Compounds

Check if the same lab product or an alternative is used in the 5 most similar protocols
The target compounds AS-19, 2a and 2b were optimized using the LigPrep tool and energy minimized using the OPLS3e force field in Schrodinger’s Small-Molecule Drug discovery suite [19 –23 ]. The individual compounds in their protonated forms were docked into the homology model of the 5-HT7R using the Induced Fit Docking workflow and the results depicted in Figs. 3–4.
Onyameh E.K., Ofori E., Bricker B.A., Gonela U.M., Eyunni S.V., Kang H.J., Voshavar C, & Ablordeppey S.Y. (2021). Design and discovery of a high affinity, selective and β-arrestin biased 5-HT7 Receptor Agonist. Medicinal chemistry research : an international journal for rapid communications on design and mechanisms of action of biologically active agents, 31(2), 274-283.
+ Open protocol
+ Expand
8

In Silico Drug Screening and Validation for SMYD3 Inhibition

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
We implemented the Small Molecule Drug Discovery Suite (Schrodinger, Inc., New York, NY, USA) to predict the binding affinity of a library of 137,990 molecules [15 (link),16 (link),17 (link)]. This library of molecules was downloaded from the free ZINC15 database, and included all “purchasable” molecules with reported or predicted activity in vitro [30 (link)]. The 3D structure of SMYD3 used for in silico docking was uploaded from the Protein Data Bank (PDB) under PDB identification code 5EX3 [31 (link)]. After an initial simulation which docked each molecule into SMYD3′s protein-target binding pocket (not its s-adenosylmethionine binding pocket), the top ten hits (most-negative binding energy) were entered into the ZINC15 molecular similarity search engine, and the 50 most-similar compounds to each of the ten leading candidates were again scored using the Schrodinger software (500 total compounds). From this iteration, the top five compounds were purchased and assessed in vitro using SMYD3 methyltransferase assays. After initial experiments, Inhibitor-4 was found to be the most promising and, consequently, it advanced to the cell line experiments described below.
Alshiraihi I.M., Jarrell D.K., Arhouma Z., Hassell K.N., Montgomery J., Padilla A., Ibrahim H.M., Crans D.C., Kato T.A, & Brown M.A. (2020). In Silico/In Vitro Hit-to-Lead Methodology Yields SMYD3 Inhibitor That Eliminates Unrestrained Proliferation of Breast Carcinoma Cells. International Journal of Molecular Sciences, 21(24), 9549.
+ Open protocol
+ Expand
9

Elaborated Aminothiazole Fragments Docking

Check if the same lab product or an alternative is used in the 5 most similar protocols
Docking of elaborated aminothiazole fragments was performed using Small Molecule Drug Discovery Suite (Release 2015-1, Schrödinger, LLC.), including Glide (version 6.6), LigPrep (version 3.3), Epik (version 3.1), and Maestro (version 10.1). Briefly, ligands were prepared with LigPrep using the OPLS_2005 force field[34 ] and charge states predicted at pH 7.0 using Epik. The compounds were desalted and all possible chiralities were created to a total of 32 per ligand. Compound conformations used for induced-fit docking[35 (link), 36 (link)] were generated using conformational search with the OPLS_2005 force field. Charge state was taken from the structure and all other settings were default for multi-ligand preparation. The protein structure (PDB: 4P2T) was prepared using the protein preparation wizard per the default settings. The binding site centroid (defined with residues 76, 87,109, and 193) in an attempt to encapsulate the entire putative binding site. All other parameters were left to default settings.
Gable J.E., Lee G.M., Acker T.M., Hulce K.R., Gonzalez E.R., Schweigler P., Melkko S., Farady C.J, & Craik C.S. (2016). Fragment-based protein-protein interaction antagonists of a viral dimeric protease. ChemMedChem, 11(8), 862-869.
+ Open protocol
+ Expand
10

Optimizing CHK2 Inhibitor Docking Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols
The crystal structure of human CHK2 in complex with ADP, debromohymnialdisine-derived inhibitors and NSC 109555 was retrieved from the Protein Data Bank (PDB: 2CN5, 2CN08, 2W07 [33 (link), 34 (link)]). To generate an optimally performing docking protocol, ADP and NSC 109555 were re-docked to the ADP-binding pocket of the crystal structure of human CHK2 (PDB: 2CN5, 2CN08, 2W07) with several combinations of scoring and algorithms for docking function using the Schrödinger Small-molecule Drug Discovery Suite. This docking protocol was subsequently applied to the Diversity Set II compound library (DTP/NIH).
Gokare P., Navaraj A., Zhang S., Motoyama N., Sung S.S, & Finnberg N.K. (2016). Targeting of Chk2 as a countermeasure to dose-limiting toxicity triggered by topoisomerase-II (TOP2) poisons. Oncotarget, 7(20), 29520-29530.
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!