Computational investigations of polymerase enzymes: Structure, function, inhibition, and biotechnology

Abstract

DNA and RNA polymerases (Pols) are central to life, health, and biotechnology because they allow the flow of genetic information in biological systems. Importantly, Pol function and (de)regulation are linked to human diseases, notably cancer (DNA Pols) and viral infections (RNA Pols) such as COVID‐19. In addition, Pols are used in various applications such as synthesis of artificial genetic polymers and DNA amplification in molecular biology, medicine, and forensic analysis. Because of all of this, the field of Pols is an intense research area, in which computational studies contribute to elucidating experimentally inaccessible atomistic details of Pol function. In detail, Pols catalyze the replication, transcription, and repair of nucleic acids through the addition, via a nucleotidyl transfer reaction, of a nucleotide to the 3′‐end of the growing nucleic acid strand. Here, we analyze how computational methods, including force‐field‐based molecular dynamics, quantum mechanics/molecular mechanics, and free energy simulations, have advanced our understanding of Pols. We examine the complex interaction of chemical and physical events during Pol catalysis, like metal‐aided enzymatic reactions for nucleotide addition and large conformational rearrangements for substrate selection and binding. We also discuss the role of computational approaches in understanding the origin of Pol fidelity—the ability of Pols to incorporate the correct nucleotide that forms a Watson–Crick base pair with the base of the template nucleic acid strand. Finally, we explore how computations can accelerate the discovery of Pol‐targeting drugs and engineering of artificial Pols for synthetic and biotechnological applications. This article is categorized under: Structure and Mechanism > Reaction Mechanisms and Catalysis Structure and Mechanism > Computational Biochemistry and Biophysics Software > Molecular Modeling

Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2

“…To evaluate the degree of fitness of the enzyme, we used the same procedure to predict the RNA Pol II activation barrier (see Figure 4 ), getting a value of 17.8 kcal mol −1 for ATP, in good agreement with experimental estimates. 37 , 38 This value is ∼1.5 kcal/mol higher than that of the viral RdRp (see Figure 4 A), demonstrating that despite its short evolutionary trajectory, the efficiency of SARS-Cov-2 RdRp is at least similar to those of highly evolved eukaryotic polymerases. 39 , 40 , 41 …”

Local Structural Dynamics at the Metal-Centered Catalytic Site of Polymerases is Critical for Fidelity

“…Comparisons with other Pols corroborate these mechanistic findings, suggesting that the structural dynamics of local elements at the catalytic site can significantly affect the ability of Pols to incorporate noncanonical base pairs. These results may have implications in drug discovery and in the rational design of catalysts for the polymerization of modified or synthetic nucleotides. , …”

“…The fidelity of DNA polymerase (Pol) enzymes refers to their ability to precisely duplicate the original template during DNA synthesis, − with implications in biology, drug discovery, and biotechnology. − Mechanistically, high-fidelity Pols efficiently select the correct deoxyribonucleoside triphosphate (dNTP) from solution and add it to the 3′-end of the growing primer strand, forming a canonical Watson–Crick (WC) base pair. In contrast, low-fidelity Pols synthesize DNA strands with errors and variations (base mutations), some of which are linked to diseases like cancer .…”

Quercetin and luteolin are single-digit micromolar inhibitors of the SARS-CoV-2 RNA-dependent RNA polymerase

“…The protease M pro catalyzes the proteolysis of polyproteins translated from the viral genome. The RdRp enzyme is responsible for the replication of RNA from an RNA template 7 , 8 . Therefore, RdRp is a nonstructural protein that plays a crucial role in the virus life cycle, acting during the viral replication and transcription processes 3 , 4 , 9 , 10 .…”