Methods and systems for organic solute sampling of aqueous and heterogeneous environments

Patent metadata

Field	Value
Publication number	US-2016357945-A1
Application number	US-201515114599-A
Country	US
Kind code	A1
Filing date	Jan 29, 2015
Priority date	Jan 29, 2014
Publication date	Dec 8, 2016
Grant date	—

Abstract

Provided are computer implemented methods for organic solute sampling in aqueous and heterogeneous environments using oscillating chemical potentials in Grand Canonical Monte Carlo simulations. The methods involve GCMC of both the solutes and water, with the excess chemical potential (μ ex ) of both the solute and the water oscillated to attain their target concentrations in the simulation system. In some example methods, the μ ex of the water and solutes over the GCMC iterations are varied to improve solute exchange probabilities and the spatial distributions of the solutes and molecular dynamics (MD) simulations may be performed in addition to GCMC to improve sampling of spatial distributions. These methods may be used to determine the hydration free energy (HFE) of the individual or multiple solutes when targeting in aqueous solutions. Also included are methods of driving solute sampling in and around macromolecules, including proteins, in aqueous environments.

First claim

1 . A computational method for sampling the spatial distribution of one or more solutes and water in a defined region of space (system) comprising:
1) assigning a target concentration, N tgt , of each of the one or more solutes and water; 2) sampling the spatial distribution of the one or more solutes and water in a computationally defined region of space using Grand-Canonical Monte-Carlo (GCMC) Metropolis sampling criteria, wherein the excess chemical potential (μ ex ) assigned for each of the one or more solutes, if present, and water is set to 0, if present; 3) updating μ ex of each of the one or more solutes and water from the difference in current concentration in the defined region of space (N sys ) and the target (N tgt ), 4) repeating steps 2) and 3) using the updated values of μ ex in step 2) to obtain a spatial distribution of the one or more solutes and water.

2 . The method according to claim 1 wherein the system contains water and one solute and where the target concentration of the solute and water is set at 1 M and 55 M, respectively, from which the hydration free energy of the solute is obtained from the value of μ ex

3 . The method according to claim 2 , wherein the system contains water and one or more solutes.

4 . The method according to claim 1 , wherein the system further comprises one or more macromolecules.

5 . The method according to claim 4 , wherein the spatial distribution of one or more solutes or water is used to identify preferential affinity of each of the solutes or water to each of the one or more macromolecules.

6 . The method according to claim 5 , wherein said one or more macromolecules are selected from a protein, RNA, DNA, carbohydrate, lipid, organic chemical, inorganic chemical, or a combination thereof.

7 . The method according to claim 4 , wherein the molecular weight of said one or more macromolecules are greater than or equal to 1000 daltons.

8 . The method according to claim 4 , wherein the μ ex of one or more solutes and water is alternately increased and decreased during the GCMC operations across consecutive cycles involving steps 2 )- 4 ), after the concentration of the solutes and the water reach their target value.

9 . The method according to claim 1 , wherein the GCMC steps are equally divided between each of the one or more solutes and water.

10 . The method according to claim 1 , wherein, the proportion of GCMC steps for each of the one or more solutes and water is assigned based on the target concentration of each of the solutes and water.

11 . The method according to claim 1 , wherein the system containing the solutes and or water is encompassed in a larger system containing said solutes and or water.

12 . The method according to claim 11 wherein the system containing the solutes and water is a sphere that is encompassed in a larger sphere whose difference in the radii is 5 A.

13 . The method according to claim 11 wherein the system additionally includes one or more macromolecules.

14 . The method according to claim 1 , wherein the GCMC is performed 2,000-50,000 times.

15 . The method according to claim 1 , wherein the spatial distribution following step 2 ) is sampled with a molecular dynamics simulation.

16 . The method of claim 1 , wherein said method is used to assist with computer-aided drug design.

17 . The method according to claim 1 , wherein μ ex is increased or decreased equal to N tgt /N sys .

18 . The method according to claim 1 , wherein μ ex is increased when N sys is lower than the N tgt and decreased when N sys is greater than N tar

19 . The method according to claim 1 wherein said computationally defined region comprises an inner region containing the one or more solutes and water, located within a larger outer region containing additional water.

20 . The method according to claim 19 wherein the difference between the inner region and outer region is large enough to limit edge effects.

21 . The method according to claim 1 wherein an output of the spatial distributions of the one or more solutes and water is generated.

Assignees

• Univ Maryland

Inventors

• Mackerell Jr Alexander D
• Raman E Prabhu
• Lakkaraju Sirish Kaushik

Classifications

• G06F17/18

  for evaluating statistical data {, e.g. average values, frequency distributions, probability functions, regression analysis (forecasting specially adapted for a specific administrative, business or logistic context G06Q10/04)} · CPC title

• G16C20/50 Primary

  Molecular design, e.g. of drugs · CPC title

• G16C10/00

  Computational theoretical chemistry, i.e. ICT specially adapted for theoretical aspects of quantum chemistry, molecular mechanics, molecular dynamics or the like · CPC title

• G16C20/30 Primary

  Prediction of properties of chemical compounds, compositions or mixtures · CPC title

• G06F19/701

  Physics · mapped topic