Molecular Modeling for Systems Pharmacology:

Integrative modeling of biomolecular assemblies and networks

1/20/15

Andrej Sali (sali@salilab.org)

While it may be hard to live with generalization, it is inconceivable to live without it. Peter Gay, Schnitzler’s Century (2002).

Contents

1. Hierarchy of biological organization and systems pharmacology

2. Modeling

3. Integrative modeling of assembly structures

4. Integrative modeling of molecular networks

Contents

1. Hierarchy of biological organization and systems pharmacology

2. Modeling

3. Integrative modeling of assembly structures

4. Integrative modeling of molecular networks

Hierarchy of biological organization

ORGANISM POPULATION

Representation: molecular structure (particles in space), localization (contents of volume elements), networks of components, inter-compartmental flows, …

Drug Discovery / Pharmacology

Drug Discovery / Pharmacology

Systems Pharmacology to the rescue

http://www.nigms.nih.gov/Training/Documents/SystemsPharmaWPSorger2011.pdf

What is Systems Pharmacology?

1. Systems pharmacology is the application of systems biology principles to the field of pharmacology. It seeks to understand how medicines work on various systems of the body. Instead of considering the effect of a drug to be the result of one specific drug-protein interaction, systems pharmacology considers the effect of a drug to be the outcome of the network of interactions a drug may have. (Wikipedia)

2. Systems Pharmacology brings a new combination of mathematical and experimental tools to bear on the discovery and analysis of therapeutic drugs. System-level understanding of pharmacological effects will help to identify new uses for existing drugs, identify those patients most likely to benefit from mono and combination therapies, and make drug discovery and development faster, cheaper, and more predictable. (http://isp.hms.harvard.edu)

Systems Pharmacology Bibliography

1. Sorger, P. (2011). Quantitative and Systems Pharmacology in the Post-genomic Era: New Approaches to Discovering Drugs and Understanding Therapeutic Mechanisms (http://www.nigms.nih.gov/Training/Documents/SystemsPharmaWPSorger2011.pdf)

2. Dar, A. C., Das, T. K., Shokat, K. M., & Cagan, R. L. (2013). Chemical genetic discovery of targets and anti-targets for cancer polypharmacology. Nature, 486(7401), 80–84.

3. Csermely, P., Korcsmáros, T., Kiss, H. J. M., London, G., & Nussinov, R. (2013). Pharmacology & Therapeutics. Pharmacology and Therapeutics, 138(3), 333–408.

4. Zhao, S., & Iyengar, R. (2012). Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action. Annual Review of Pharmacology and Toxicology, 52(1), 505–521.

5. L Kapitzky, P Beltrao, TJ Berens, N Gassner, Ci Zhou, A Wuster, J Wu, MM Babu, SJ Elledge, D Toczyski, RS Lokey and NJ Krogan. Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action. Molecular Systems Biology 6:451, 2010.

6. http://isp.hms.harvard.edu

7. http://www.nature.com/psp

Contents

1. Hierarchy of biological organization and systems pharmacology

2. Modeling

3. Integrative modeling of assembly structures

4. Integrative modeling of molecular networks

Scientific progress

1. Iteration of Hypothesis and Experiment

HypothesisModel

Experiment

Scientific progress

1. Iteration of Hypothesis and Experiment

HypothesisModel

Experiment

Hypothesis vs Theory

Scientific progress

1. Iteration of Hypothesis and Experiment

HypothesisModel

Experiment

Thomas Kuhn, 1962. The Structure of Scientific Revolutions

Hypothesis vs Theory

Scientific progress

1. Iteration of Hypothesis and Experiment

HypothesisModel

Experiment

Thomas Kuhn, 1962. The Structure of Scientific Revolutions

2. Exploratory research (eg, genome sequencing).

Hypothesis vs Theory

Modeling

Scientific modelling is a scientific activity the aim of which is to make a particular part or feature of the world easier to understand, define, quantify, visualize, or simulate. It requires selecting and identifying relevant aspects of a situation in the real world and then using different types of models for different aims, such as conceptual models to better understand, operational models to operationalize, mathematical models to quantify, and graphical models to visualize the subject. Modelling is an essential and inseparable part of scientific activity, and many scientific disciplines have their own ideas about specific types of modeling. (Wikipedia)

Composition Stoichiometry Chemical complementarity

X-ray diffraction

Composition Stoichiometry Chemical complementarity

X-ray diffraction

To understand and modulate cellular processes, we need their models.

These models are best generated by considering all available information.

1. Hierarchy of biological organization and systems pharmacology

2. Modeling

3. Integrative modeling of assembly structures

4. Integrative modeling of molecular networks

Contents

Structural biology: Maximize accuracy, resolution, completeness, and efficiency of the

structural coverage of macromolecular assemblies

Motivation: Models will allow us to understand how machines work, how they evolved, how they can be controlled, modified, and perhaps even designed.

There may be thousands of biologically relevant macromolecular complexes whose structures are yet to be characterized, involved in a few hundred core biological processes.

GroEL chaperonin

flagellar motorHIV virus

nuclear pore complexATP synthase ribosome

tRNA synthetaseRNA polymerase II

02/15/2007

Sali A, Earnest T, Glaeser R, Baumeister W. From words to literature in structural proteomics. Nature 422, 216-225, 2003. Ward A, Sali A, Wilson I. Integrative structural biology. Science 339, 913-915, 2013.

PHYSICS

STATISTICSEXPERIMENT

∫

Integrative Structural Biology for maximizing accuracy, resolution, completeness, and efficiency of structure determination

Use structural information from any source: measurement, first principles, rules; resolution: low or high resolution

to obtain the set of all models that are consistent with it.

INTUITION

Gatheringinformation

Analyzing modelsand information

Samplinggood models

Designing modelrepresentationand evaluation

A description of integrative structure determinationAlber et al. Nature 450, 683-694, 2007

Robinson et al. Nature 450, 974-982, 2007Alber et al. Annual Reviews in Biochemistry 77, 11.1–11.35, 2008

Russel et al. PLoS Biology 10, 2012Ward et al. Science 339, 913-915, 2013

Schneidman et al. Curr.Opin.Str.Biol., 2014.

While it may be hard to live with generalization, it is inconceivable to live without it. Peter Gay, Schnitzler’s Century (2002).

Challenges in interpreting the data in terms of a structural model

• Sparseness due to incompleteness of measurements

• Error due to measurement and other imperfections

• Ambiguity eg, due to multiple copies of a protein in a system

• Incoherence (mixture) due to multiple states of a system in a heterogenous sample

Pushing the envelope of structural biology by integration of all available information

• Size

• Static systems in single and multiple states

• Dynamic systems

• Bulk and single molecule views

• Impure samples

• Overlapping with other domains such as systems biology

Prot

ein

Sh

ape

Protein Stoichiometry

Protein-protein Proximities Symmetry

Protein Localization

Configuration of 456 proteins in the Nuclear Pore Complex

Alber et al. Nature 450, 684-694, 2007. Alber et al. Nature 450, 695-702, 2007.

with M. Rout & B. Chait

Prot

ein

Sh

ape

Protein Stoichiometry

Protein-protein Proximities Symmetry

Protein Localization

Configuration of 456 proteins in the Nuclear Pore Complex

Alber et al. Nature 450, 684-694, 2007. Alber et al. Nature 450, 695-702, 2007.

with M. Rout & B. Chait

Open source, versions, documentation, wiki, examples, mailing lists, unit testing, bug tracking, ...

Integrative Modeling Platform (IMP) http://integrativemodeling.org

D. Russel, K. Lasker, B. Webb, J. Velazquez-Muriel, E. Tjioe, D. Schneidman, F. Alber, B. Peterson, A. Sali, PLoS Biol, 2012. R. Pellarin, M. Bonomi, B. Raveh, S. Calhoun, C. Greenberg, G.Dong.

IMP C++/Python library

restrainer

Simplicity

Flex

ibili

ty

Domain-specific

Chimera

Model

angle restraint

volume restraint

conjugate gradients

Monte Carlo

harmonic

nonbonded list

particledistance score

IO

connectivity restraint

cross correlation

Domino

rigid bodySAXS

docking

molecule

Representation: Atomic Rigid bodies Coarse-grained Multi-scale Symmetry / periodicity Multi-state systems

Scoring: Density maps EM images Proteomics FRET Chemical and Cys cross-linking Homology-derived restraints SAXS Native mass spectrometry Statistical potentials Molecular mechanics forcefields Bayesian scoring Library of functional forms (ambiguity, ...)

Analysis: Clustering Chimera Pymol PDB files Density maps

Sampling: Simplex Conjugate Gradients Monte Carlo Brownian Dynamics Molecular Dynamics Replica Exchange Divide-and-conquer enumeration

Modeling aspects

Sampling and scoring

1.Representation

2.Scoring function

3.Sampling algorithm

4.Assessment

Find simplest possible models that reproduce the measured data within their uncertainty.

Representation

1 5 10 20 40 60 100

Ignorance (residues per bead)

Hierarchical model representation facilitates using imprecise information

X structure d measured data point i f computed data point i (forward model) w weight of data point i

Scoring function: Least-squares modeling of a structure

S(X) = wii∑ [di − fi (X)]

2i

i

i

When , we get a “maximum likelihood” approach,

for which .

wi = 1/σ i2

S(X) = χ 2

S

ΔD

Scoring function: Bayesian modeling of structure(s)

Model M can include coordinates of one or more structures X as well as additional parameters (noise levels, weights, calibration parameters, ...).

likelihoodposterior prior

D � f(M)

Likelihood is the probability density of observing data D, given model M and prior information I (by relying on a model of noise and a forward model, which computes data D given model M).

Prior is the probability density of model M, given prior information I.

Posterior is the probability density of model M, given data D and information I.

Rieping, Habeck, Nilges. Science, 2005

M model D data I prior information f(M) forward model

p(AB) = p(BA) = p(A) ⋅ p(B/A) = p(B) ⋅ p(A/B)

Sampling, optimization, enumeration

Sampling, optimization, enumeration

Assessment(in the absence of Bayesian inference)

1.Existence of a good-scoring model.

Assessment(in the absence of Bayesian inference)

1.Existence of a good-scoring model.

2.Precision of the ensemble of good-scoring models.

Assessment(in the absence of Bayesian inference)

1.Existence of a good-scoring model.

2.Precision of the ensemble of good-scoring models.

3.Check model against unused data (cross-validation).

Assessment(in the absence of Bayesian inference)

1.Existence of a good-scoring model.

2.Precision of the ensemble of good-scoring models.

3.Check model against unused data (cross-validation).

4.Known precision / accuracy for “similar” cases.

Assessment(in the absence of Bayesian inference)

1.Existence of a good-scoring model.

2.Precision of the ensemble of good-scoring models.

3.Check model against unused data (cross-validation).

4.Known precision / accuracy for “similar” cases.

5.Non-random patterns in the model.

Assessment(in the absence of Bayesian inference)

1.Existence of a good-scoring model.

2.Precision of the ensemble of good-scoring models.

3.Check model against unused data (cross-validation).

4.Known precision / accuracy for “similar” cases.

5.Non-random patterns in the model.

Assessment

Modeling facilitates assessing the data as well as models in terms of precision and accuracy.

(in the absence of Bayesian inference)

05/27/2006

Steps in Comparative Protein Structure Modeling

No

Target – Template Alignment MSVIPKRLYGNCEQTSEEAIRIEDSPIV---TADLVCLKIDEIPERLVGE

ASILPKRLFGNCEQTSDEGLKIERTPLVPHISAQNVCLKIDDVPERLIPE

Model Building

START

ASILPKRLFGNCEQTSDEGLKIERTPLVPHISAQNVCLKIDDVPERLIPERASFQWMNDK

TARGET

Template Search

TEMPLATE

OK?

Model Evaluation

END

Yes

M. Marti-Renom et al. Ann. Rev. Biophys. Biomolec. Struct. 29, 291, 2000. N. Eswar et al. Curr. Protocols Bioinformatics 5.6, 2006. http://salilab.org/

1. Hierarchy of biological organization and systems pharmacology

2. Modeling

3. Integrative modeling of assembly structures

4. Integrative modeling of molecular networks

Contents

Integrating structural biology and systems biology

∫CJ Ryan, P Cimermancic, ZA Szpiech, A Sali, RD Hernandez, NJ Krogan Nat Gen 14, 2013.

Annotation of enzyme function

1. Prediction of the function in the context of the pathway

2. Prediction of the pathway based on all available information

3. Automated (ie, thorough, objective, …) method

Computational Geometry Lab   Tel-Aviv University, Israel

Mapping  the  Phase  Space  of  Models  for  Transport  through  the  NPC

What is the pathway, given a set of potential enzymes and metabolites as well as at least one enzyme and/or metabolite in it?

Integrative determination of metabolic pathways based on structure and systems information

Proteomics Chemogenomics

Virtual screening Cheminformatics

Genome neighborhood

Protein interaction predictions

Gene coexpression

High-throughput screening

Metabolomics

AAATTGGTA CAAATGGTA CAAATGGTA ATATTGGTT

Regulons

+( )

Structural biology• Virtual screening (VS)• In silico transformations and chemical

similarity calculations• High-throughput screening

Systems biology and imaging• Coexpression of genes • Genome context • Genetic interactions • Metabolite levels • Protein functional links • Orthology • Tomography • Super-resolution optical microscopy • FRET spectroscopy

A tiny subset of structure-, imaging- and systems-based information that (in principle) informs network prediction

Components

Mindset: From integrative structure modeling towards integrative pathway mapping

Sampling and scoring

Model

Cross-linking

Restraints

Co-purification Bioinformatics, physics

Electron microscopy

NMRX-ray crystallography

Small angle X-ray scattering

Proteomics HDXMS

Sali et al. Nature, 2003

Alber et al. Nature, 2007

Robinson et al. Nature, 2007

Alber et al. Annual Reviews in Biochemistry, 2008

Russel et al. PLoS Biology, 2012

Ward et al. Science, 2013

IMP

Components

Mindset: From integrative structure modeling towards integrative pathway mapping

Sampling and scoring

Complex Topology

Model

Cross-linking

Restraints

Co-purification Bioinformatics, physics

Electron microscopy

NMRX-ray crystallography

Small angle X-ray scattering

Proteomics HDXMS

Sali et al. Nature, 2003

Alber et al. Nature, 2007

Robinson et al. Nature, 2007

Alber et al. Annual Reviews in Biochemistry, 2008

Russel et al. PLoS Biology, 2012

Ward et al. Science, 2013

IMP

Components

Mindset: From integrative structure modeling towards integrative pathway mapping

Sampling and scoring

Biological network

Model

Cross-linking

Restraints

Co-purificationDocking Bioinformatics, physics

Electron microscopy

NMRX-ray crystallography

Cheminformatics

Operon/genome context

IMPPotential

Components

Mindset: From integrative structure modeling towards integrative pathway mapping

Sampling and scoring

Metabolic Pathway

Model

Cross-linking

Restraints

Co-purificationDocking Bioinformatics, physics

Electron microscopy

NMRX-ray crystallography

Cheminformatics

Operon/genome context

IMPPotential

Representation

• Enzymes and ligands are individual nodes

• Edges reflect a relationship between an enzyme and its substrate/product

Pathway model represented as a graph

Scoring• Translation of information into restraints that quantify the degree of

consistency between a pathway model and the corresponding information • Scoring function is a sum of individual restraints to rank alternative models

Similarity ensemble approach (SEA) E-value

Chemical similarity between transformed substrate and product

Virtual screening (VS)docking score Similarity to screening hits

Sampling Monte Carlo with simulated annealing

1) Starting with a model, select a node to alter identity

2) Select a new node identity from all possible node identities & make change in model

3) If change improves score, accept the new model. Otherwise, accept the new model with a probability determined by the difference in scores.

4) Repeat until “convergence”

ΔS = Score(modeli+1) - Score(modeli)Prob. of acceptance = exp(-ΔS/T)

Example I: reconstructing glycolysis

1kinase

2isomerase

3kinase

4aldolase

5isomerase

6dehydrogenase

7kinase

8mutase

9enolase

10kinase

Here, we are treating glycolysis as a linear pathway

Four-stage overview Glycolysis

Docking data from: Chakrapani Kalyanaraman and Matthew P. Jacobson, Biochemistry 49, 4003, 2010. SEA calculations by Magdalena Korczynska, Henry Lin, and Brian Shoichet

Gatheringinformation

Analyzing models and information

Samplinggood models

Designing modelrepresentationand evaluation

• Assessing top models over 3.5 standard deviations above mean

• Monte Carlo with simulated annealing 5 M iterations per run & 400 runs

• 2,742 potential substrates & products • 10 glycolytic enzymes • Docking scores for ligand-enzyme pairs • SEA e-values between all enzymes • Chemical transformation scores for all

substrate-enzyme-product trios

• Fixed-length graph: 10 protein nodes and 11 ligand nodes

Assessment: reconstructing enzyme order Glycolysis

Ord

ered

by

frequ

ency

at a

eac

h po

sitio

n

Correct Pathway (Position in pathway →)

1 2 3 4 5 6 7 8 9 10

Predicted Pathways

1 2 3 4 5 6 7 8 9 10

5 1 2 3 4

Step in pathway

Rank by VS score alone

Rank using VS scores

Rank using chemical

transformations

Rank using VS, chemical

transformations, and SEA

1 19 20 54 1

2 60 54 27 1

3 12 10 93 1

4 86 175 83 1

5 6 3 2 1

6 165 369 3 1

7 47 163 1 1

8 3 50 1 1

9 11 7 1 1

10 72 43 1 1

Assessment: synergy of different types of information Glycolysis

Step in pathway

Rank by VS score alone

Rank using VS scores

Rank using chemical

transformations

Rank using VS, chemical

transformations, and SEA

1 19 20 54 1

2 60 54 27 1

3 12 10 93 1

4 86 175 83 1

5 6 3 2 1

6 165 369 3 1

7 47 163 1 1

8 3 50 1 1

9 11 7 1 1

10 72 43 1 1

Assessment: synergy of different types of information Glycolysis

Step in pathway

Rank by VS score alone

Rank using VS scores

Rank using chemical

transformations

Rank using VS, chemical

transformations, and SEA

1 19 20 54 1

2 60 54 27 1

3 12 10 93 1

4 86 175 83 1

5 6 3 2 1

6 165 369 3 1

7 47 163 1 1

8 3 50 1 1

9 11 7 1 1

10 72 43 1 1

Assessment: synergy of different types of information Glycolysis

Step in pathway

Rank by VS score alone

Rank using VS scores

Rank using chemical

transformations

Rank using VS, chemical

transformations, and SEA

1 19 20 54 1

2 60 54 27 1

3 12 10 93 1

4 86 175 83 1

5 6 3 2 1

6 165 369 3 1

7 47 163 1 1

8 3 50 1 1

9 11 7 1 1

10 72 43 1 1

Assessment: synergy of different types of information Glycolysis

Prediction of pathway downstream of H. influenzae RdAW SBP TRAP transporter

TRAP transporter

dehydrogenase

UxuR (regulator)

dehydratase

aldolasekinase reductase

Haemophilus influenzae

Tripartite ATP-independent periplasmic transporters - family of transporters in bacteria and archaea for the uptake of organic acids

“Bacterial flu” found in the upper respiratory system of host

Centers for Disease Control and Prevention

Virtual screening Chemical transformations

Genome neighborhood

High-throughput screening

+( )Gathering information

Sampling good models

Designing model representation and evaluation

Pathway model

Analyzing models and information

Potential ligands Potential proteins

Similarity ensemble approach

Metabolic endpoints

…

6 protein-ligand pairs

5 enzymatic reactions

1 protein screened

1 endpoint 6 proteins6 proteins

Monte Carlo simulated annealing

Assessing sampling Assessing accuracy

Validated SPB TRAP pathway prediction

in vitro assays by Daniel Wichlecki, Gerlt lab Structure by Matthew Vetting et al., NYSGXRC

Metformin “network”Viollet, B., Guigas, B., Sanz Garcia, N., Leclerc, J., Foretz, M., & Andreelli, F. (2011). Cellular and molecular mechanisms of metformin: an overview. Clinical Science, 122(6), 253–270.

In ConclusionThe goal is a comprehensive description of the multitude of interactions between molecular entities, which in turn is a prerequisite for the discovery of general structural principles that underlie all cellular processes.

Sali, Earnest, Glaeser, Baumeister. From words to literature in structural proteomics. Nature 422, 216-225, 2003. Robinson, Sali, Baumeister. The molecular sociology of the cell. Nature 450, 974-982, 2007. Alber, Foerster, Korkin, Topf, Sali. Annual Reviews in Biochemistry 77, 11.1–11.35, 2008. D. Russel et al. “Putting the pieces together: integrative structure determination of macromolecular assemblies”. PLoS Biol., 2012. A. Ward, A. Sali A, I. Wilson. Integrative structural biology. Science 339, 913-915, 2013. Schneidman, Pellarin, Sali. Uncertainty in integrative structural modeling. Curr. Opin. Str. Biol., 96-104, 2014.

This goal will be achieved by a formal integration of experiment, physics, and statistical inference, spanning all relevant size and time scales.