Compound Design
Fragment Growing
Boltzmann Maps has many ways of updating the structure and composition of a compound. Many such abilities are available through the methods discussed in the Structure Manipulation section. However, in this section we will focus on fragment-based compound design.
Theory
A great deal of discussion on the theory of Fragment-Based-Drug Design (FBDD) and its uses in BMaps can be found in our Technology section and publications [1,2,3]. Here though, we wish to provide some useful clarity on terminology and concepts related to performing FBDD in BMaps.
Fragment - A fragment is a small molecule, most often without rotatable bonds, and with attachment points, that may be bound to a specified point on another compound either directly or via a linking chemical group.
While not always true, and not a limitation set by BMaps on user imported fragments, the following bounds are often put on the classification of fragments:
- A molecular weight of <300 Da
- Fewer than three hydrogen-bond donors and acceptors
- Fewer than three rotatable bonds
- A cLogP of ≤3
- Heavy atom counts tend to be limited to <20
Chemical Potential - The amount of change to the Gibbs free energy caused by changing the number of a particle type (atoms, molecules, etc) in the system while keeping the number of other particle types and the system temperature and pressure constant. This can then be used to determine how likely a particle (or fragment in the case of BMaps) will stay in the system or as its current form.
Simulated Annealing - Simulated Annealing is a process, often cited as deriving from metallurgy or glass making, during which the system is heated, given energy, or excited to a state of such high energy that all possible states are occupied. During the process of "cooling" the system, the probability of the system still occupying a higher energy state decrease until a global optima or approximation of a global optima is found. Though at infinite time bounds on cooling a global optima is mathematically guaranteed, this is often impractical and an approximation to the global optima is accepted.
Simulated Annealing of Chemical Potentials - In SACP, a parameter B for a given fragment or general particle is annealed. B is related to the excess chemical potential (The non-ideal portion of the chemical potential for the species) of the species by:
B = μ'/kBT + ln()
Where μ' is the excess chemical potential, kB is the Boltzmann constant, T is the temperature, and is the average particle number.
Fragment Map
In the case of fragment growing, SACP is used in conjunction with Monte Carlo type techniques to perform a Grand Canonical simulation for a given fragment type [4]. Here we flood the area around a protein and/or compound with fragments at a high B value and excess chemical potential. Multiple sample snapshots of the fragments at a given B value are taken to conform to rigorous Boltzmann energy statistics. This distribution of fragment positions with respect to the environment of the protein or ligand is called a Fragment Map. As the excess chemical potential in the system decreases, only the most stable fragments on the surface of the protein remain. This information can be used to find hot spots, high affinity binding positions, and, when lined up with a compound in a similar location, linked to the compound to create a more active molecule.
Fragment Maps in BMaps have already been pre-computed for over 500 proteins from the PDB using 136 fragments plus water. BMaps users are also able to create new fragment maps for different protein-fragment combinations.
The following sections will broadly outline how to design compounds, especially in hit-to-lead contexts, using fragment growing.
Terminal Replacements
If you right click a terminal atom (including atoms only terminated by hydrogen) you will see a replace terminal section of the drop down menu. Below a few of the most common replacements is the option to expand the menu for more common molecular termination groups. If you have more unique changes, refer to the Compound Editor found in the Compounds Selector menu options.
Grow with Fragment
Compounds made visible in the main window of BMaps ("3D Workspace") can be grown using fragment map results. The sections below walk you through the process of growing a compound with fragments. If you would like to explore use cases and scientific thinking around fragment growing, check out our recorded webinars, blogs, or chat directly with us in the BMaps Community Slack.
Right Click Menu
Right clicking on a compound atom in the 3D Workspace will provide a dropdown with the Grow with fragment sub-menu. Rick clicking also shows a cyan arrow the indicates the direction the fragment will grow off of that atom. If the arrow points towards another atom in the compound, then that portion of the compound will be replaced with the selected fragment. Ctrl or Cmd plus right click will switch the direction of the cyan arrow. Pressing Shift(Alt)-Ctrl(Cmd)-right-click will change which bond the fragment grows along if there are multiple options.
Once you are happy with the growth vector, you can select an option from the sub-menu.
Other Menu States
There are cases where growing with fragments are not currently supported or do not make clear sense. For these, menu messages will explain what is happening. The following menu messages are currently shown:
Can't grow from this atom
Ring substitutions are not currently supported
Only single bonded atom replacements are currently supported
Best Pose
Only the best pose, as determined by existing at the most negative B value, for each fragment that can attach at the vector and is marked as Searchable in the Manage Fragments menu will be displayed.
Distribution
This will show the distribution of poses, limited by the user selected threshold B value, for each fragment that can attach at the vector and is marked as Searchable in the Manage Fragments menu. The distribution are shown as slightly transparent ghosts. The currently selected fragment will be fully opaque.
Fragment Set
Grow with Fragment Set is a quick method to select some common fragment sets if you do not wish to use all fragments, which is the default, or else your own imported fragment set. The contents of each fragment set can be seen in the Fragment Manager menu.
Post Fragment Search Menu - Distribution
The fragment growing menu that is available after performing a fragment growing search displays the fragments that are found to have a favorable binding score. The Binding Score is based on the free energy of the fragment at the most positive B value the fragment was found at. By default, only the Binding Score, Molecular Weight(Mol. Wt.), and Linker Type (Link Type) are show as columns next to each fragment (Frag). The linker type refers to the connection in between the compound growth vector atom and the fragment binding atom. Hovering over a fragment's row will show a tool tip with the name of the fragment and the most negative B value at which the fragment was found. Remember that the more negative the B value at which a fragment is found, the higher affinity the fragment has.
Additional columns including Ligand Efficiency, Interaction Energy, and Fragment attachment atom can be displayed using the checkboxes under the menu's option button. Pose buckets can also be added to the exported CSV columns if selected. Ligand Efficiency is the Binding Score divided by the number of heavy atoms in the fragment.
Additional options include:
· Add multiple fragments - Don't close the fragment menu when you add one fragment to the compound.
· Showing fragment hydrogens
· Highlighting the binding score with a Target or Off-Target Threshold value. Note that the binding scores related to targets will be highlighted in green if the value is more negative (Read: Favorable) than the threshold, or not highlighted otherwise. Fragments with favorable binding scores for Off-Target proteins will be highlighted in red and otherwise not highlighted. Multiple binding scores will only show if there are multiple proteins in the 3D Workspace.
· In pose selector, sort poses by binding score
In order to change how the fragments are viewing in the menu, you can click the crossing arrows button to switch between 2D chemical structure and chemical names.
The download csv icon in the upper right will save all of the information from the fragment run to your local machine.
The dropdown arrows to the right of each fragment row will open the pose selector slider below the respective fragment row. Hovering the dropdown arrow with tell you how many favorable poses that could be linked to the compound via the specified linking molecule in along the provided vector were found of this fragment. The pose selector slider can be used to update the opaque fragment in the 3D workspace. The tool tip will update with the Binding Score and Interaction energy for each of the poses as the slider is moved. If there is only one pose available the pose selector will not move.
Like elsewhere in BMaps, selecting the pin icon 
will add the row to the 3D workspace. Selecting the plus icon 
will grow the compound with that row's fragment. Note, unless the Add multiple fragments box is checked in the options menu, the fragment growing menu will close after clicking the plus button. Clicking the plus button will create a new compound with the fragment grown onto the compound as specified. With Add multiple fragments selected, each selection of the plus button will create a new compound in the Compound Selector menu.
If at any point you want to change which fragments are being search, the Manage searchable frags at the top of the fragment growing menu will open the Fragment Manager menu.
Post Fragment Search Menu
The fragment growing menu when the best pose is desired is the same as the distribution menu except that you cannot select specific poses to grow from.
Fragment Data Query
To perform a more advanced fragment search, you can click on the Fragment data query option from the right click dropdown menu. Doing so will open a menu that will allow you to specify the radius to search for fragments in, the B value acceptable threshold, specific fragments by name, or fragment sets you wish to use and not use.
Fragment Manager
The Fragment Manager menu allows users to select fragments they do or do not want to see in fragment growing searches or to be used in determining Hotspots.
At the top of the window are selectors for All Simulated Fragments, Fragment Search, and Hotspots. Selecting one will show either all fragments, only those marked as searchable, or only those used for calculating hotspots respectively. The Quick filter text box will filter the list based on words in the fragment name, set, or library. The Quick filter requires at least two letters to begin filtering. The dropdown to the right of the filter text box allows you to filter based on specific fragment sets. If you add any filters, a Clear all filters button will appear above the fragment set or library filter dropdown that can be clicked to remove all filters.
In the upper right part of the manager is a Select all or Deselect all button. When any fragment rows are selected (indicated by a checkmark next to the Fragment Name on the left), the dropdown to the right of the Deselect all button becomes active and allows you to perform group selections or deselections of search ability and hotspot inclusion. To the right of that is the Choose columns button which lets you select which properties of the fragments you would like to display.
Each column displayed may be filtered on by clicking the funnel icons next to the column name. The columns may be sorted in ascending or descending order by clicking on the column name. The choices of filters will determine which fragments are used for BMaps calculations and can always be reset with the All Simulated Fragments button.
Additional Features
Not available in the regular BMaps interface is an option to grow a compound along all vectors with all possible fragments. If you have a use for this feature or wish to see a demo, please reach out.
The BMaps team is constantly developing our fragment based drug design capabilities. If you have an idea let us know.