Richard Bryce

Richard Bryce, BSc, PhD, FRSC CChem

Dr

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Personal profile

Overview

 The work in Richard Bryce's group is aimed at developing computational models to improve the accuracy with which molecular processes are described and understood in the condensed phase and then to integrate and employ these methods in the drug design and development process, involving collaboration with medicinal chemists, biochemists and biologists.

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His research interests involve the development and application of accurate and efficient computational methods for structure-based drug design. A major focus of his work is the theoretical investigation of carbohydrate structure, energetics, dynamics and reactivity. This requires accurate treatment of aqueous solvent, which as led to the development and application of solvent models to carbohydrate analogue systems. The group employs a variety of computational techniques, including molecular simulation and hybrid quantum mechanical (QM)/molecular mechanical (MM) models.

 We also maintain the AMBER parameter database, an archive of AMBER force field parameters.

 More about the group and its research can be found in the "My Group" and "Research and Projects" tabs.

Biography

Richard Bryce heads up the computational-aided drug design group in the Division of Pharmacy and Optometry.  He is a Reader in Biomedicinal Chemistry, having studied chemistry at St. Andrews University (BSc, 1995) and computational chemistry at Manchester University (PhD, 1998).  He was a Robert Lincoln MacNeil scholar at the University of Pennsylvania (1992-1993) and a Ramsay Memorial Fellow at the University of Manchester (1999-2001).  His work receives support from a variety of sources, including EPSRC, The Wellcome Trust, MRC, BBSRC and the Royal Society.  He is a fellow of the Royal Society of Chemistry and member and former chair of the Molecular Graphics and Modelling Society.

Research interests

The work in Richard Bryce's group is aimed at developing computational models to improve the accuracy with which molecular processes are described and understood in the condensed phase and then to integrate and employ these methods in the drug design and development process, involving collaboration with medicinal chemists, biochemists and biologists.

His research interests involve the development and application of accurate and efficient computational methods for structure-based drug design. A major focus of his work is the theoretical investigation of carbohydrate structure, energetics, dynamics and reactivity. This requires accurate treatment of aqueous solvent, which as led to the development and application of solvent models to carbohydrate analogue systems. The group employs a variety of computational techniques, including molecular simulation and hybrid quantum mechanical (QM)/molecular mechanical (MM) models.

Proteins

1. Simulation of biomolecular dynamics and thermodynamics

In addition to hybrid QM/MM models, we also have explored more empirical approaches to modelling biomolecular recognition. For example, we have used a combined molecular mechanics and continuum solvent approach to calculation of thermodynamics, leading to new insights into the recognition of oligosaccharides by the protein, concanavalin A. We have used a similar approach to predict fluorophore-DNA interactions pertinent to molecular diagnostics. This method has been extended to evaluate the free energies of binding of closely-related ligands, with a view to application in rational drug design.

2. Computer-aided drug design

CADD

We seek to apply our knowledge of modelling ligand-receptor interactions to adopt a computationally-led design of small molecule modulators. We currently use a range of computational techniques, for example mapping, de novo methods and virtual screening (using molecular docking). In this way, we pursue a number of multidisciplinary design projects, collaborating with medicinal chemists, biochemists and biologists: one example is our structure-based virtual screening of compound libraries which led to the identification of a novel non-nucleobase-derived inhibitor of human thymidine phosphorylase, an anti-cancer target, as a candidate for lead optimisation.

3. Modelling carbohydrates

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Carbohydrates, the most naturally abundant biomolecule, function in a number of roles, from maintaining structural integrity to providing energy-storage. However, it is the centrality of carbohydrates in biomolecular recognition, mediating events such as cell-cell interaction and the immune response that offers major opportunities for therapeutic intervention. These polar flexible molecules expose many of the shortcomings of current computational modeling methods.We use a range of methods to study the energetics and dynamics of carbohydrates in the condensed phase. In particular, we have explored the use of combined QM/MM potentials and molecular dynamics. To enable the calculation of free energy surfaces, in collaboration we have derived a focused semi-empirical QM Hamiltonian to specifically improve modelling of carbohydrates.

My group

RABRichard Bryce

Principal Investigator

 

 

 

Jas Kalayan

Postdoctoral fellow 

 

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Aya Emam

PhD student

 

 

 

ismaeel

Sanjida Faiza

PhD student

 

 

 

ismaeel Sondos Musleh

PhD student

 

 

 

 

LK

Linghan Kong

PhD student

 

 

 

CH

Sherihan El-Sayed

PhD student

 

 

 

Megan Eadsforth

PhD student

  

 

 

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Heng Cao

PhD student 

 

 

Chao-Yu Yang

PhD student 

yzAzam (Solmaz) Nesabi

PhD student 

 

 

 

yzJuliette Newell

PhD student 

 

 

2022

(year 2022): Bryce group and Leach group meal

 

Other group members

2019

 (year 2018): Rupesh Chikhale, Fai Alkathiri, Solmaz Nesabi, Jess Horsfield, Jake Bowdem Linghan Kong, Clara Humann, Yang Zhang, Richard Bryce, Ismaeel Ramzan (front left, clockwise)

 (year 2015, from the left): Mohammad Ghattas and Mrs Ghattas, Abdul Wadood, Irfan Alibay, Kepa Burusco-Goni, Alessio Atzori, Panichakorn Jaiyong, Rasha Alqus, Hoda Abdel-Aal Bettley

 2010

(year 2010): Alessio Atzori, Richard Bryce, Mohammad Ghattas, Daniel Mucs, Waleed Zalloum, Biljana Arsic (back)

Neil Bruce, Luz Flores-Michel, Hoda Abdel-Aal Bettley (front)

oldgp

(year 2008): Neil Bruce, Qiantao Wang, Walleed Zalloum, Daniel Mucs, Hoda Abdel-Aal Bettley (back row, left to right)

Mohammad Ghattas, Richard Bryce, Vijay Manickam Achari (front row, left to right)

 

older

(year 2003): Gabriel Marks, Gavin Seddon, Pascal Bonnet, Abdul-Mueed Muslim (left to right)

  • Dr Ismaeel Ramzan (postgraduate)
  • Dr Ebru Aksanoglu (postgraduate)
  • Sara Al-Rawashdeh (MPhil postgraduate)
  • Clara Humann (MPhil postgraduate)
  • Dr Md Ataul Islam (postdoc)
  • Dr Rupesh Chikhale (postdoc)
  • Yang Zhang (MPhil postgraduate)
  • Dr Irfan Alibay (postgraduate)
  • Dr Rasha Alqus (postgraduate)
  • Dr Panichakorn Jaiyong (postgraduate)
  • Dr Alessio Atzori (postgraduate)
  • Dr Luz Flores-Michel (postgraduate)
  • Dr Kepa Burusco-Goni (postdoc)
  • Dr Daniel Mucs (postgraduate)
  • Dr Mohammad Ghattas (postgraduate)
  • Dr Qiantao Wang (postgraduate)
  • Dr Pedro Fong (postgraduate)
  • Dr Felicity Mitchell (postgraduate)
  • Dr Vijay Manickam Achari (visiting postgraduate)
  • Dr Abdul-Mueed Muslim (postdoc)
  • Dr Gabriel Marks (postdoc/postgraduate)
  • Dr Mehdi Rajabi (postgraduate)
  • Dr Noor Atatreh (postgraduate)
  • Dr Joao Neres (associate member)
  • Prof Pascal Bonnet (postdoc)
  • Dr Virginia McNally (postgraduate)
  • Dr Teoh Chong (visiting postgrduate)
  • Dr Qiantao Wang (postgraduate)
  • Dr Pedro Fong (postgraduate)

Teaching

  • Physics of Intermolecular Forces, Protein-Ligand Interactions, Computational Aspects of Rational Drug Design (Molecular Simulation, De Novo Design, Docking, Virtual Screening, QSAR)

Expertise related to UN Sustainable Development Goals

In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):

  • SDG 3 - Good Health and Well-being
  • SDG 7 - Affordable and Clean Energy

Research Beacons, Institutes and Platforms

  • Digital Futures
  • Institute for Data Science and AI

Keywords

  • Computational chemistry, Computer-aided molecular design, molecular dynamics, quantum chemistry, molecular recognition, binding affinities

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