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Byareddy SN, Sharma K, Sachdev S, Reddy AS, Acharya A, Klaustermeier KM, Lorson CL, Singh K. Potential therapeutic targets for Mpox: the evidence to date. Expert Opin Ther Targets 2023; 27:419-431. [PMID: 37368464 PMCID: PMC10722886 DOI: 10.1080/14728222.2023.2230361] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/07/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
INTRODUCTION The global Mpox (MPX) disease outbreak caused by the Mpox virus (MPXV) in 2022 alarmed the World Health Organization (WHO) and health regulation agencies of individual countries leading to the declaration of MPX as a Public Health Emergency. Owing to the genetic similarities between smallpox-causing poxvirus and MPXV, vaccine JYNNEOS, and anti-smallpox drugs Brincidofovir and Tecovirimat were granted emergency use authorization by the United States Food and Drug Administration. The WHO also included cidofovir, NIOCH-14, and other vaccines as treatment options. AREAS COVERED This article covers the historical development of EUA-granted antivirals, resistance to these antivirals, and the projected impact of signature mutations on the potency of antivirals against currently circulating MPXV. Since a high prevalence of MPXV infections in individuals coinfected with HIV and MPXV, the treatment results among these individuals have been included. EXPERT OPINION All EUA-granted drugs have been approved for smallpox treatment. These antivirals show good potency against Mpox. However, conserved resistance mutation positions in MPXV and related poxviruses, and the signature mutations in the 2022 MPXV can potentially compromise the efficacy of the EUA-granted treatments. Therefore, MPXV-specific medications are required not only for the current but also for possible future outbreaks.
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Affiliation(s)
- Siddappa N Byareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | | | - Shrikesh Sachdev
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Athreya S. Reddy
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | | | - Christian L Lorson
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Kamal Singh
- Department of Pharmaceutical Chemistry, DPSRU, New Delhi-110017
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
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Kannan SR, Sachdev S, Reddy AS, Kandasamy SL, Byrareddy SN, Lorson CL, Singh K. Mutations in the monkeypox virus replication complex: Potential contributing factors to the 2022 outbreak. J Autoimmun 2022; 133:102928. [PMID: 36252459 PMCID: PMC9562781 DOI: 10.1016/j.jaut.2022.102928] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/01/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Attributes contributing to the current monkeypox virus (MPXV) outbreak remain unknown. It has been established that mutations in viral proteins may alter phenotype and pathogenicity. To assess if mutations in the MPXV DNA replication complex (RC) contribute to the outbreak, we conducted a temporal analysis of available MPXV sequences to identify mutations, generated a DNA replication complex (RC) using structures of related viral and eukaryotic proteins, and structure prediction method AlphaFold. Ten mutations within the RC were identified and mapped onto the RC to infer role of mutations. Two mutations in F8L (RC catalytic subunit), and two in G9R (a processivity factor) were ∼100% prevalent in the 2022 sequences. F8L mutation L108F emerged in 2022, whereas W411L emerged in 2018, and persisted in 2022. L108 is topologically located to enhance DNA binding affinity of F8L. Therefore, mutation L108F can change the fidelity, sensitivity to nucleoside inhibitors, and processivity of F8L. Surface exposed W411L likely affects the binding of regulatory factor(s). G9R mutations S30L and D88 N in G9R emerged in 2022, and may impact the interaction of G9R with E4R (uracil DNA glycosylase). The remaining six mutations that appeared in 2001, reverted to the first (1965 Rotterdam) isolate. Two nucleoside inhibitors brincidofovir and cidofovir have been approved for MPXV treatment. Cidofovir resistance in vaccinia virus is achieved by A314T and A684V mutations. Both A314 and A684 are conserved in MPXV. Therefore, resistance to these drugs in MPXV may arise through similar mechanisms.
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Affiliation(s)
| | - Shrikesh Sachdev
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Athreya S. Reddy
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | | | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198, USA,Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Christian L. Lorson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA,Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden,Corresponding author. 471g, Bond Life Sciences Center, 1201 E Rollins Street, Columbia, MO, 65211, USA
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Craggs TD, Sustarsic M, Plochowietz A, Mosayebi M, Kaju H, Cuthbert A, Hohlbein J, Domicevica L, Biggin PC, Doye JPK, Kapanidis AN. Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase. Nucleic Acids Res 2020; 47:10788-10800. [PMID: 31544938 PMCID: PMC6846080 DOI: 10.1093/nar/gkz797] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 09/02/2019] [Accepted: 09/18/2019] [Indexed: 01/23/2023] Open
Abstract
DNA-binding proteins utilise different recognition mechanisms to locate their DNA targets; some proteins recognise specific DNA sequences, while others interact with specific DNA structures. While sequence-specific DNA binding has been studied extensively, structure-specific recognition mechanisms remain unclear. Here, we study structure-specific DNA recognition by examining the structure and dynamics of DNA polymerase I Klenow Fragment (Pol) substrates both alone and in DNA–Pol complexes. Using a docking approach based on a network of 73 distances collected using single-molecule FRET, we determined a novel solution structure of the single-nucleotide-gapped DNA–Pol binary complex. The structure resembled existing crystal structures with regards to the downstream primer-template DNA substrate, and revealed a previously unobserved sharp bend (∼120°) in the DNA substrate; this pronounced bend was present in living cells. MD simulations and single-molecule assays also revealed that 4–5 nt of downstream gap-proximal DNA are unwound in the binary complex. Further, experiments and coarse-grained modelling showed the substrate alone frequently adopts bent conformations with 1–2 nt fraying around the gap, suggesting a mechanism wherein Pol recognises a pre-bent, partially-melted conformation of gapped DNA. We propose a general mechanism for substrate recognition by structure-specific enzymes driven by protein sensing of the conformational dynamics of their DNA substrates.
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Affiliation(s)
- Timothy D Craggs
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Marko Sustarsic
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Anne Plochowietz
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Majid Mosayebi
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.,School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran 19538-33511, Iran
| | - Hendrik Kaju
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Andrew Cuthbert
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen 6708 WE, The Netherlands.,Microspectroscopy Research Facility Wageningen, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Laura Domicevica
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
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Bhardwaj A, Ghose D, Thakur KG, Dutta D. Escherichia coli β-clamp slows down DNA polymerase I dependent nick translation while accelerating ligation. PLoS One 2018; 13:e0199559. [PMID: 29924849 PMCID: PMC6010275 DOI: 10.1371/journal.pone.0199559] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/08/2018] [Indexed: 11/25/2022] Open
Abstract
The nick translation property of DNA polymerase I (Pol I) ensures the maturation of Okazaki fragments by removing primer RNAs and facilitating ligation. However, prolonged nick translation traversing downstream DNA is an energy wasting futile process, as Pol I simultaneously polymerizes and depolymerizes at the nick sites utilizing energy-rich dNTPs. Using an in vitro assay system, we demonstrate that the β-clamp of the Escherichia coli replisome strongly inhibits nick translation on the DNA substrate. To do so, β-clamp inhibits the strand displacement activity of Pol I by interfering with the interaction between the finger subdomain of Pol I and the downstream primer-template junction. Conversely, β-clamp stimulates the 5’ exonuclease property of Pol I to cleave single nucleotides or shorter oligonucleotide flaps. This single nucleotide flap removal at high frequency increases the probability of ligation between the upstream and downstream DNA strands at an early phase, terminating nick translation. Besides β-clamp-mediated ligation helps DNA ligase to seal the nick promptly during the maturation of Okazaki fragments.
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Affiliation(s)
- Amit Bhardwaj
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | | | - Dipak Dutta
- CSIR-Institute of Microbial Technology, Chandigarh, India
- * E-mail:
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Rutvisuttinunt W, Meyer PR, Scott WA. Interactions between HIV-1 reverse transcriptase and the downstream template strand in stable complexes with primer-template. PLoS One 2008; 3:e3561. [PMID: 18974785 PMCID: PMC2570493 DOI: 10.1371/journal.pone.0003561] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Accepted: 10/09/2008] [Indexed: 11/18/2022] Open
Abstract
Background Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) forms stable ternary complexes in which RT is bound tightly at fixed positions on the primer-template (P/T). We have probed downstream interactions between RT and the template strand in the complex containing the incoming dNTP (+1 dNTP•RT•P/T complex) and in the complex containing the pyrophosphate analog, foscarnet (foscarnet•RT•P/T complex). Methods and Results UV-induced cross-linking between RT and the DNA template strand was most efficient when a bromodeoxyuridine residue was placed in the +2 position (the first template position downstream from the incoming dNTP). Furthermore, formation of the +1 dNTP•RT•P/T complex on a biotin-containing template inhibited binding of streptavidin when biotin was in the +2 position on the template but not when the biotin was in the +3 position. Streptavidin pre-bound to a biotin residue in the template caused RT to stall two to three nucleotides upstream from the biotin residue. The downstream border of the complex formed by the stalled RT was mapped by digestion with exonuclease RecJF. UV-induced cross-linking of the complex formed by the pyrophosphate analog, foscarnet, with RT and P/T occurred preferentially with bromodeoxyuridine in the +1 position on the template in keeping with the location of RT one base upstream in the foscarnet•RT•P/T complex (i.e., in the pre-translocation position). Conclusions For +1 dNTP•RT•P/T and foscarnet•RT•P/T stable complexes, tight interactions were observed between RT and the first unpaired template nucleotide following the bound dNTP or the primer terminus, respectively.
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Affiliation(s)
- Wiriya Rutvisuttinunt
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Peter R. Meyer
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Walter A. Scott
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- * E-mail:
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Kukreti P, Singh K, Ketkar A, Modak MJ. Identification of a new motif required for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I (Klenow fragment): the RRRY motif is necessary for the binding of single-stranded DNA substrate and the template strand of the mismatched duplex. J Biol Chem 2008; 283:17979-90. [PMID: 18448432 DOI: 10.1074/jbc.m801053200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Klenow fragment of Escherichia coli DNA polymerase I houses catalytic centers for both polymerase and 3'-5' exonuclease activities that are separated by about 35 A. Upon the incorporation of a mismatched nucleotide, the primer terminus is transferred from the polymerase site to an exonuclease site designed for excision of the mismatched nucleotides. The structural comparison of the binary complexes of DNA polymerases in the polymerase and the exonuclease modes, together with a molecular modeling of the template strand overhang in Klenow fragment, indicated its binding in the region spanning residues 821-824. Since these residues are conserved in the "A" family DNA polymerases, we have designated this region as the RRRY motif. The alanine substitution of individual amino acid residues of this motif did not change the polymerase activity; however, the 3'-5' exonuclease activity was reduced 2-29-fold, depending upon the site of mutation. The R821A and R822A/Y824A mutant enzymes showed maximum cleavage defect with single-stranded DNA, mainly due to a large decrease in the ssDNA binding affinity of these enzymes. Mismatch removal by these enzymes was only moderately affected. However, data from the exonuclease-polymerase balance assays with mismatched template-primer suggest that the mutant enzymes are defective in switching mismatched primer from the polymerase to the exonuclease site. Thus, the RRRY motif provides a binding track for substrate ssDNA and for nonsubstrate single-stranded template overhang, in a polarity-dependent manner. This binding then facilitates cleavage of the substrate at the exonuclease site.
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Affiliation(s)
- Pinky Kukreti
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey Medical School and Graduate School of Biomedical Sciences, Newark, NJ 07103, USA
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Singh K, Srivastava A, Patel SS, Modak MJ. Participation of the Fingers Subdomain of Escherichia coli DNA Polymerase I in the Strand Displacement Synthesis of DNA. J Biol Chem 2007; 282:10594-604. [PMID: 17259182 DOI: 10.1074/jbc.m611242200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The replication of the genome requires the removal of RNA primers from the Okazaki fragments and their replacement by DNA. In prokaryotes, this process is completed by DNA polymerase I by means of strand displacement DNA synthesis and 5 '-nuclease activity. Here, we demonstrate that the strand displacement DNA synthesis is facilitated by the collective participation of Ser(769), Phe(771), and Arg(841) present in the fingers subdomain of DNA polymerase I. The steady and presteady state kinetic analysis of the properties of appropriate mutant enzymes suggest that: (a) Ser(769) and Phe(771) together are involved in the strand separation via the formation of a flap structure, and (b) Arg(841) interacts with the template strand to achieve the optimal strand separation and DNA synthesis. The amino acid residues Ser(769) and Phe(771) are constituents of the O1-helix, which together with O and O2 helices form a 3-helix bundle structure. We note that this 3-helix bundle motif also exists in prokaryotic RNA polymerase. Thus in both DNA and RNA polymerases, this motif may have been adopted to achieve the strand separation function.
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Affiliation(s)
- Kamalendra Singh
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry-New Jersey Medical School, Newark, New Jersey 07103, USA.
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Datta K, Wowor AJ, Richard AJ, LiCata VJ. Temperature dependence and thermodynamics of Klenow polymerase binding to primed-template DNA. Biophys J 2006; 90:1739-51. [PMID: 16339886 PMCID: PMC1367323 DOI: 10.1529/biophysj.105.071837] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Accepted: 11/10/2005] [Indexed: 11/18/2022] Open
Abstract
DNA binding of Klenow polymerase has been characterized with respect to temperature to delineate the thermodynamic driving forces involved in the interaction of this polymerase with primed-template DNA. The temperature dependence of the binding affinity exhibits distinct curvature, with tightest binding at 25-30 degrees C. Nonlinear temperature dependence indicates Klenow binds different primed-template constructs with large heat capacity (DeltaCp) values (-870 to -1220 cal/mole K) and thus exhibits large temperature dependent changes in enthalpy and entropy. Binding is entropy driven at lower temperatures and enthalpy driven at physiological temperatures. Large negative DeltaCp values have been proposed to be a 'signature' of site-specific DNA binding, but type I DNA polymerases do not exhibit significant DNA sequence specificity. We suggest that the binding of Klenow to a specific DNA structure, the primed-template junction, results in a correlated thermodynamic profile that mirrors what is commonly seen for DNA sequence-specific binding proteins. Klenow joins a small number of other DNA-sequence independent DNA binding proteins which exhibit unexpectedly large negative DeltaCp values. Spectroscopic measurements show small conformational rearrangements of both the DNA and Klenow upon binding, and small angle x-ray scattering shows a global induced fit conformational compaction of the protein upon binding. Calculations from both crystal structure and solution structural data indicate that Klenow DNA binding is an exception to the often observed correlation between DeltaCp and changes in accessible surface area. In the case of Klenow, surface area burial can account for only about half of the DeltaCp of binding.
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Affiliation(s)
- Kausiki Datta
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
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