MGMS Lecture Tour

All MGMS Seminars are free of charge and open to all.

The MGMS was formed in 1981 to bring together scientists working in different fields of study—such as chemistry, physics, biology, mathematics and computer science—who have a common interest in computational molecular modelling and molecular graphics. One of our activities is to organize MGMS Lecture Tours to highlight cutting-edge research in the field.

2020: Prof. Rebecca Wade

Prof. Rebecca Wade, ZMBH Research Group Leader, HITS (Heidelberg Institute for Theoretical Studies)
Prof. Rebecca Wade

We are pleased to announce that Prof. Rebecca Wade from Heidelberg Institute for Theoretical Studies (HITS) and Heidelberg University, Germany will be giving a virtual MGMS Lecture Tour lecture titled, “Computational Approaches to Protein Dynamics and Binding Kinetics for Drug Discovery”, and it will be held via Zoom on:

Tuesday, November 24th, 2020

  • 2:00-2:45 pm GMT:  Lecture: “Computational Approaches to Protein Dynamics and Binding Kinetics for Drug Discovery”
  • 2:45- 3:00 pm GMT: Q&A
  • 3:00 pm GMT: MGMS Annual General Meeting (AGM)

“Computational Approaches to Protein Dynamics and Binding Kinetics for Drug Discovery”

Rebecca C. Wade1,2 

  • 1Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany, 
  • 2Zentrum für Molekulare Biologie (ZMBH), DKFZ-ZMBH Alliance and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Germany 

The dynamic nature of protein structures and the diversity of protein binding pocket dynamics provide challenges and opportunities for ligand design [1]. I will present the recent development of a machine learning approach to identify pocket conformations with high druggability in TRAPP, a toolbox of computational approaches to identify TRAnsient Pockets in Proteins for ligand design (https://trapp.h-its.org/). [2]. Protein binding site flexibility is one of the factors that can affect drug-target binding kinetics. Growing evidence that the efficacy of a drug can be correlated to target binding kinetics has led to the development of many new methods aimed at computing rate constants for receptor-ligand binding processes [3,4], see also: kbbox.h-its.org. Here, I will describe our studies to explore the determinants of structure-kinetic relationships and to develop computationally efficient methods to estimate drug-target binding kinetic parameters. I will introduce the t-random acceleration molecular dynamics simulation (tRAMD) method to compute relative residence times [5] and discuss how interaction fingerprint (MD-IFP [6]) and machine learning analysis [7] of tRAMD trajectories can be used to decipher the determinants of drug-target residence times. 

  • [1] Stank A, Kokh DB, Fuller JC, Wade RC. Protein binding pocket dynamics. Acc. Chem Res., 2016, 49:809-815.  
  • [2] Yuan JH, Han SB, Richter S, Wade RC, Kokh DB, Druggability Assessment in TRAPP using Machine Learning Approaches J. Chem. Inf. Model. 2020, 60 (3), 1685-1699
  • [3] Bruce NJ, Ganotra GK, Kokh DB, Sadiq SK, Wade RC. New approaches for computing ligand-receptor binding kinetics. Curr Opin Struct Biol. 2018, 49: 1-10.
  • [4] Nunes-Alves A, Kokh DB, Wade RC. Recent progress in molecular simulation methods for drug binding kinetics Curr Opin Struct Biol. 2020, 64:126-133.
  • [5] Kokh DB, Amaral M,……Wade RC.  Estimation of drug-target residence times by t-random acceleration molecular dynamics simulations, J. Chem. Theory Comput. 2018, 14: 3859–3869.
  • [6] Kokh DB, Doser B, Richter S, Ormersbach F, Cheng X, Wade RC, 2020, arXiv:2006.11066
  • [7] Kokh DB, Kaufmann T, Kister B, Wade RC.  Machine Learning Analysis of tRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times, Frontiers. Mol. Biosci.  2019, 6: 36.

About Rebecca Wade
 
Rebecca Wade leads the Molecular and Cellular Modeling group at Heidelberg Institute for Theoretical Studies (HITS) and is Professor of Computational Structural Biology at the Center for Molecular Biology at Heidelberg University (ZMBH).  Rebecca Wade studied at Oxford University and, following postdoctoral research at the universities of Houston and Illinois, became a group leader at the European Molecular Biology Laboratory (EMBL) in Heidelberg in 1992. She moved to HITS in 2001. Rebecca Wade’s research is focused on the development and application of computer-aided methods to model and simulate biomolecular interactions. Her research group has developed novel protein structure-based methods for drug discovery and protein engineering, most recently for studying drug binding kinetics, as well as multiresolution computational approaches to investigate macromolecular association and the effects of macromolecular crowding. Rebecca Wade’s research has been published in over 250 scientific papers, as well as software programs and web servers that are used world-wide. She is an Associate Editor of the Journal of Molecular Recognition and PloS Computational Biology. She was the recipient of the 2004 Hansch Award of the QSAR and Modelling Society and the 2016 International Society of Quantum Biology and Pharmacology (ISQBP) Award in Computational Biology.  URL: www.h-its.org/mcm.

Prof. Wade, an alumna of the University of Oxford, is:

You can read more about Prof. Wade’s background and research interests.

Past MGMS Lecture Tours

2018 Dr. David Glowacki,
University of Bristol, UK
2015 Professor Dr Gisbert Schneider,
ETH Zurich, Switzerland
2014 Prof. Arthur J. Olson,
The Scripps Research Institute, La Jolla, California, USA
2012 Prof. Modesto Orozco,
Group Leader, Molecular Modelling and Bioinformatics, Institute for Research in Biomedicine (IRB Barcelona)
2011 Prof. Tim Clark,
Friedrich-Alexander-University Erlangen- Nurnberg, Germany, and
Centre for Molecular Design, University of Portsmouth