Senior Research Scientist
Nigel Richards

Education:

BSc (Hons) in Chemistry, Imperial College, University of London, UK (1980)
PhD in Organic Synthesis, University of Cambridge, UK (1983)
Harkness Fellow, Computational Chemistry, Columbia University, USA (1983-1985)

Research Summary:

My research focuses on understanding the structure, mechanism, evolution and applications of enzymes. Current projects include:

Computational investigations of residue networks that mediate energy transfer in enzymes
Structural and mechanistic characterization of enzymes that mediate C-nucleoside biosynthesis
Biocatalytic routes to novel C-nucleosides with potential use as anti-viral agents
Discovery and characterization of asparagine synthetase inhibitors as anti-cancer agents
Computational simulations of DNA and RNA containing modified nucleotides from an Artificially Expanded Genetic Information System (AEGIS)
Characterization and engineering of psychrophilic DNA polymerases and DNA ligases

Awards

Fellow, American Association for the Advancement of Science, 2010
Fellow, Royal Society of Chemistry, 2016
Honorary Fellow, Indian Society of Chemists & Biologists, 2020
Fellow, Learned Society of Wales, 2021

Recent Publications

A foundational shift for models in enzyme function
J. P. Klinman, S. M. Miller and N. G. J. Richards
J. Am. Chem. Soc.147(18) 14884-14904 (2025) 25 April: 147(18), 14884-14904. DOI:10.1021/jacs.5c02388
<Abstract>

This Perspective addresses the unresolved, and still hotly contested, question of how enzymes transition from stable enzyme-substrate (ES) complexes to successful, femtosecond barrier crossings. By extending Marcus theory to enzyme-catalyzed reactions, we argue that environmental reorganization of the protein scaffold, together with associated water molecules, achieves the intersection of reactant and product potential energy surfaces. After discussing the experimentally demonstrated importance of reduced activation enthalpy in enzyme-catalyzed transformations, we describe new methodologies that measure the temperature dependence of (i) time-averaged hydrogen/deuterium exchange into backbone amides and (ii) time-dependent Stokes shifts to longer emission wavelengths in appended chromophores at the protein/water interface. These methods not only identify specific pathways for the transfer of thermal energy from solvent to the reacting bonds of bound substrates but also suggest that collective thermally activated protein restructuring must occur very rapidly (on the ns–ps time scale) over long distances. Based on these findings, we introduce a comprehensive model for how barrier crossing takes place from the ES complex. This exploits the structural preorganization inherent in protein folding and subsequent conformational sampling, which optimally positions essential catalytic components within ES ground states and correctly places reactive bonds in the substrate(s) relative to embedded energy transfer networks connecting the protein surface to the active site. The existence of these anisotropic energy distribution pathways introduces a new dimension into the ongoing quest for improved de novo enzyme design.

Nucleic acid joining enzymes: biological functions and synthetic applications beyond DNA.
Blackstock C, Walters-Freke C, Richards N, Williamson A
Biochem J, Portland Press (2025) 22 January: 482, 39-56. DOI: 10.1042/BCJ20240136
<Abstract>

DNA-joining by ligase and polymerase enzymes has provided the foundational tools for generating recombinant DNA and enabled the assembly of gene and genome-sized synthetic products. Xenobiotic nucleic acid (XNA) analogues of DNA and RNA with alternatives to the canonical bases, so-called 'unnatural' nucleobase pairs (UBP-XNAs), represent the next frontier of nucleic acid technologies, with applications as novel therapeutics and in engineering semi-synthetic biological organisms. To realise the full potential of UBP-XNAs, researchers require a suite of compatible enzymes for processing nucleic acids on a par with those already available for manipulating canonical DNA. In particular, enzymes able to join UBP-XNA will be essential for generating large assemblies and also hold promise in the synthesis of single-stranded oligonucleotides. Here, we review recent and emerging advances in the DNA-joining enzymes, DNA polymerases and DNA ligases, and describe their applications to UBP-XNA manipulation. We also discuss the future directions of this field which we consider will involve two-pronged approaches of enzyme biodiscovery for natural UBP-XNA compatible enzymes, coupled with improvement by structure-guided engineering.

3D variability analysis reveals a hidden conformational change controlling ammonia transport in human asparagine synthetase
Coricello A, Nardone AJ, Lupia A, Gratteri C, Vos M, Chaptal V, Alcaro S, Zhu W, Takagi Y, Richards NGJ
Nat. Commun., Nature (2024) 3 December: 15(10538). DOI: 10.1038/s41467-024-54912-9
<Abstract>

Advances in X-ray crystallography and cryogenic electron microscopy (cryo-EM) offer the promise of elucidating functionally relevant conformational changes that are not easily studied by other biophysical methods. Here we show that 3D variability analysis (3DVA) of the cryo-EM map for wild-type (WT) human asparagine synthetase (ASNS) identifies a functional role for the Arg-142 side chain and test this hypothesis experimentally by characterizing the R142I variant in which Arg-142 is replaced by isoleucine. Support for Arg-142 playing a role in the intramolecular translocation of ammonia between the active site of the enzyme is provided by the glutamine-dependent synthetase activity of the R142 variant relative to WT ASNS, and MD simulations provide a possible molecular mechanism for these findings. Combining 3DVA with MD simulations is a generally applicable approach to generate testable hypotheses of how conformational changes in buried side chains might regulate function in enzymes.

The chemistry of formycin biosynthesis
Richards NGJ, Naismith JN
Front. Chem. Biol., Frontiers Media SA (2024) 11 July: 3, 1428646. DOI: 10.3389/fchbi.2024.1428646
<Abstract>

Remarkable progress has been made to elucidate the structural and mechanistic enzymology of the biosynthetic pathways that give rise to naturally occurring C-nucleosides. These compounds are generally cytotoxic and exhibit interesting antiviral, antibiotic and anti-parasitic activity. Here we review current knowledge concerning formycin biosynthesis and highlight deficiencies in our understanding of key chemical transformations in the pathway.

Arginine kinase activates arginine for phosphorylation by pyramidalization and polarization
Falcioni F, Molt RW Jr., Jin Y, Waltho JP, Hay S, Richards, NGJ, Blackburn GM
ACS Catal, ACS (2024) 16 April: 14(9), 6650-6658. DOI: 10.1021/acscatal.4c00380
<Abstract>

Arginine phosphorylation plays numerous roles throughout biology. Arginine kinase (AK) catalyzes the delivery of an anionic phosphoryl group (PO₃^–) from ATP to a planar, trigonal nitrogen in a guanidinium cation. Density functional theory (DFT) calculations have yielded a model of the transition state (TS) for the AK-catalyzed reaction. They reveal a network of over 50 hydrogen bonds that delivers unprecedented pyramidalization and out-of-plane polarization of the arginine guanidinium nitrogen (Nη2) and aligns the electron density on Nη2 with the scissile P–O bond, leading to in-line phosphoryl transfer via an associative mechanism. In the reverse reaction, the hydrogen-bonding network enforces the conformational distortion of a bound phosphoarginine substrate to increase the basicity of Nη2. This enables Nη2 protonation, which triggers PO₃^– migration to generate ATP. This polarization–pyramidalization of nitrogen in the arginine side chain is likely a general phenomenon that is exploited by many classes of enzymes mediating the post-translational modification of arginine.

Reactivity and mechanism in chemical and synthetic biology
Richards, NGJ, Bearne SL, Goto Y, Parker EJ
Phil. Trans. R. Soc. B Biol. Sci., The Royal Society Publishing (2023) 27 February: 378(1871), 20220023. DOI: 10.1098/rstb.2022.0023
<Abstract>

Physical organic chemistry and mechanistic thinking provide a strong intellectual framework for understanding the chemical logic of evolvable informational macromolecules and metabolic transformations in living organisms. These concepts have also led to numerous successes in designing and applying tools to delineate biological function in health and disease, chemical ecology and possible alternative chemistries employed by extraterrestrial life. A symposium at the 2020 Pacifichem meeting was scheduled in December 2020 to discuss designing and exploiting expanded genetic alphabets, methods to understand the biosynthesis of natural products and re-engineering primary metabolism in bacteria. The COVID-19 pandemic led to postponement of in-person discussions, with the symposium eventually being held on 20–21 December 2021 as an online event. This issue is a written record of work presented on biosynthetic pathways and enzyme catalysis, engineering microorganisms with new metabolic capabilities, and the synthesis of non-canonical, nucleobases for medical applications and for studies of alternate chemistries for living organisms. The variety of opinion pieces, reviews and original research articles provide a starting point for innovations that clarify how complex biological systems emerge from the rules of chemical reactivity and mechanism.

Experimental and computational snapshots of C-C bond formation in a C-nucleoside synthase
Li W, Girt GC, Radadiya A, Stewart JJP, Richards NGJ, Naismith JN
Open Biology, The Royal Society Publishing (2023) 11 January: 13(1), 220287. DOI: 10.1098/rsob.220287
<Abstract>

The biosynthetic enzyme, ForT, catalyses the formation of a C-C bond between 4-amino-1H-pyrazoledicarboxylic acid and MgPRPP to produce a C-nucleoside precursor of formycin A. The transformation catalysed by ForT is of chemical interest because it is one of only a few examples in which C-C bond formation takes place via an electrophilic substitution of a small, aromatic heterocycle. In addition, ForT is capable of discriminating between the aminopyrazoledicarboxylic acid and an analogue in which the amine is replaced by a hydroxyl group; a remarkable feat given the steric and electronic similarities of the two molecules. Here we report biophysical measurements, structural biology and quantum chemical calculations that provide a detailed molecular picture of ForT-catalysed C-C bond formation and the conformational changes that are coupled to catalysis. Our findings set the scene for employing engineered ForT variants in the biocatalytic production of novel, anti-viral C-nucleoside and C-nucleotide analogues.

Development of triazole-conjugated dihydropyrimidinone (DHPM) derivatives as potential P-glycoprotein inhibitors
Bijani S, Shaikh F, Mirza D, Siu SWI, Jain N, Ferreira RJ, dos Santos DJVA, Rawal R, Richards NGJ, Shah A, Radadiya A
ACS Omega, ACS (2022) 17 May: 7(19), 16278-16287. DOI: 10.1021/acsomega.1c05839
<Abstract>

P-glycoprotein (Pgp), an ATP binding cassette (ABC) transporter, is an ATP-dependent efflux pump responsible for cancer multidrug resistance. As part of efforts to identify human Pgp (hPgp) inhibitors, we prepared a series of novel triazole-conjugated dihydropyrimidinones using a synthetic approach that is well suited for obtaining compound libraries. Several of these dihydropyrimidinone derivatives modulate human P-glycoprotein (hPgp) activity with low micromolar EC50 values. Molecular docking studies suggest that these compounds bind to the M-site of the transporter.

Functional characterization of two PLP-dependent enzymes involved in capsular polysaccharide biosynthesis from Campylobacter jejuni
Riegert AS, Narindoshvili T, Coricello A, Richards NGJ, Raushel FM
Biochemistry, ACS (2021) 21 September: 60(19), 2836-2843. DOI: 10.1021/acs.biochem.1c00439
<Abstract>

Campylobacter jejuni is a Gram-negative, pathogenic bacterium that causes campylobacteriosis, a form of gastroenteritis. C. jejuni is the most frequent cause of food-borne illness in the world, surpassing Salmonella and E. coli. Coating the surface of C. jejuni is a layer of sugar molecules known as the capsular polysaccharide that, in C. jejuni NCTC 11168, is composed of a repeating unit of d-glycero-l-gluco-heptose, d-glucuronic acid, d-N-acetyl-galactosamine, and d-ribose. The d-glucuronic acid moiety is further amidated with either serinol or ethanolamine. It is unknown how these modifications are synthesized and attached to the polysaccharide. Here, we report the catalytic activities of two previously uncharacterized, pyridoxal phosphate (PLP)-dependent enzymes, Cj1436 and Cj1437, from C. jejuni NCTC 11168. Using a combination of mass spectrometry and nuclear magnetic resonance, we determined that Cj1436 catalyzes the decarboxylation of l-serine phosphate to ethanolamine phosphate. Cj1437 was shown to catalyze the transamination of dihydroxyacetone phosphate to (S)-serinol phosphate in the presence of l-glutamate. The probable routes to the ultimate formation of the glucuronamide substructures in the capsular polysaccharides of C. jejuni are discussed.

Building better polymerases: Engineering the replication of expanded genetic alphabets
Ouaray, Z., Benner, S. A., Georgiadis, M. M., Richards, N. G. J.
J. Biol. Chem., ASBMB (2020) 11 December: 295(50):17046-17059, DOI:10.1074/jbc.REV120.013745
<Abstract>

DNA polymerases are today used throughout scientific research, biotechnology, and medicine, in part for their ability to interact with unnatural forms of DNA created by synthetic biologists. Here especially, natural DNA polymerases often do not have the "performance specifications" needed for transformative technologies. This creates a need for science-guided rational (or semi-rational) engineering to identify variants that replicate unnatural base pairs (UBPs), unnatural backbones, tags, or other evolutionarily novel features of unnatural DNA. In this review, we provide a brief overview of the chemistry and properties of replicative DNA polymerases and their evolved variants, focusing on the Klenow fragment of Taq DNA polymerase (Klentaq). We describe comparative structural, enzymatic, and molecular dynamics studies of WT and Klentaq variants, complexed with natural or noncanonical substrates. Combining these methods provides insight into how specific amino acid substitutions distant from the active site in a Klentaq DNA polymerase variant (ZP Klentaq) contribute to its ability to replicate UBPs with improved efficiency compared with Klentaq. This approach can therefore serve to guide any future rational engineering of replicative DNA polymerases.

(View publication page for Nigel Richards)

Senior Research Scientist
Nigel Richards

Education:

Research Summary:

Awards

Recent Publications

Photo

Interests

Contact

Senior Research Scientist Nigel Richards

Education:

Research Summary:

Awards

Recent Publications

Photo

Interests

Contact

Senior Research Scientist
Nigel Richards