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  1. AU="Mainan, Avijit"
  2. AU="Basu-Modak, Sharmila"
  3. AU="Talik, I."
  4. AU="Pendleton, Andrew D"
  5. AU="Wikström, G"
  6. AU="YW Smart"
  7. AU="Lafayette, Christa"
  8. AU="Parry, Christopher M"

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  1. Article ; Online: Dynamic Counterion Condensation Model Decodes Functional Dynamics of RNA Pseudoknot in SARS-CoV-2: Control of Ion-Mediated Pierced Lasso Topology.

    Mainan, Avijit / Roy, Susmita

    The journal of physical chemistry letters

    2023  Volume 14, Issue 46, Page(s) 10402–10411

    Abstract: The programmed frameshifting stimulatory element, a promising drug target for COVID-19 treatment, involves a RNA pseudoknot (PK) structure. This RNA PK facilitates frameshifting, enabling RNA viruses to translate multiple proteins from a single mRNA, ... ...

    Abstract The programmed frameshifting stimulatory element, a promising drug target for COVID-19 treatment, involves a RNA pseudoknot (PK) structure. This RNA PK facilitates frameshifting, enabling RNA viruses to translate multiple proteins from a single mRNA, which is a key strategy for their rapid evolution. Overcoming the challenges of capturing large-scale structural changes of RNA under the influence of a dynamic counterion environment (K
    MeSH term(s) Humans ; RNA ; SARS-CoV-2/genetics ; Frameshifting, Ribosomal ; Nucleic Acid Conformation ; COVID-19 Drug Treatment ; COVID-19
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2023-11-13
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.3c02755
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Influence of ion and hydration atmospheres on RNA structure and dynamics: insights from advanced theoretical and computational methods.

    Sarkar, Raju / Mainan, Avijit / Roy, Susmita

    Chemical communications (Cambridge, England)

    2024  Volume 60, Issue 27, Page(s) 3624–3644

    Abstract: RNA, a highly charged biopolymer composed of negatively charged phosphate groups, defies electrostatic repulsion to adopt well-defined, compact structures. Hence, the presence of positively charged metal ions is crucial not only for RNA's charge ... ...

    Abstract RNA, a highly charged biopolymer composed of negatively charged phosphate groups, defies electrostatic repulsion to adopt well-defined, compact structures. Hence, the presence of positively charged metal ions is crucial not only for RNA's charge neutralization, but they also coherently decorate the ion atmosphere of RNA to stabilize its compact fold. This feature article elucidates various modes of close RNA-ion interactions, with a special emphasis on Mg
    MeSH term(s) RNA/chemistry ; Water/chemistry ; Computer Simulation ; Metals
    Chemical Substances RNA (63231-63-0) ; Water (059QF0KO0R) ; Metals
    Language English
    Publishing date 2024-03-28
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1472881-3
    ISSN 1364-548X ; 1359-7345 ; 0009-241X
    ISSN (online) 1364-548X
    ISSN 1359-7345 ; 0009-241X
    DOI 10.1039/d3cc06105a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Dynamic effects of the spine of hydrated magnesium on viral RNA pseudoknot structure.

    Ramachandran, Vysakh / Mainan, Avijit / Roy, Susmita

    Physical chemistry chemical physics : PCCP

    2022  Volume 24, Issue 39, Page(s) 24570–24581

    Abstract: In the cellular environment, a viral RNA Pseudoknot (PK) structure is responsive to its prevailing ion atmosphere created by a mixture of monovalent and divalent cations. We investigate the influence of such a mixed-salt environment on RNA-PK structure ... ...

    Abstract In the cellular environment, a viral RNA Pseudoknot (PK) structure is responsive to its prevailing ion atmosphere created by a mixture of monovalent and divalent cations. We investigate the influence of such a mixed-salt environment on RNA-PK structure at an atomic resolution through three sets of 1.5 μs explicit solvent molecular dynamics (MD) simulations and also by building a dynamic counterion-condensation (DCC) model at varying divalent Mg
    MeSH term(s) Cations, Divalent ; Ligands ; Magnesium/chemistry ; Nucleic Acid Conformation ; Phosphates ; RNA/chemistry ; RNA, Viral/chemistry ; Solvents
    Chemical Substances Cations, Divalent ; Ligands ; Phosphates ; RNA, Viral ; Solvents ; RNA (63231-63-0) ; Magnesium (I38ZP9992A)
    Language English
    Publishing date 2022-10-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d2cp01075e
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Acquired resistance to KRAS G12C small-molecule inhibitors via genetic/nongenetic mechanisms in lung cancer.

    Mohanty, Atish / Nam, Arin / Srivastava, Saumya / Jones, Jeff / Lomenick, Brett / Singhal, Sharad S / Guo, Linlin / Cho, Hyejin / Li, Aimin / Behal, Amita / Mirzapoiazova, Tamara / Massarelli, Erminia / Koczywas, Marianna / Arvanitis, Leonidas D / Walser, Tonya / Villaflor, Victoria / Hamilton, Stanley / Mambetsariev, Isa / Sattler, Martin /
    Nasser, Mohd W / Jain, Maneesh / Batra, Surinder K / Soldi, Raffaella / Sharma, Sunil / Fakih, Marwan / Mohanty, Saswat Kumar / Mainan, Avijit / Wu, Xiwei / Chen, Yihong / He, Yanan / Chou, Tsui-Fen / Roy, Susmita / Orban, John / Kulkarni, Prakash / Salgia, Ravi

    Science advances

    2023  Volume 9, Issue 41, Page(s) eade3816

    Abstract: Inherent or acquired resistance to sotorasib poses a substantialt challenge for NSCLC treatment. Here, we demonstrate that acquired resistance to sotorasib in isogenic cells correlated with increased expression of integrin β4 (ITGB4), a component of the ... ...

    Abstract Inherent or acquired resistance to sotorasib poses a substantialt challenge for NSCLC treatment. Here, we demonstrate that acquired resistance to sotorasib in isogenic cells correlated with increased expression of integrin β4 (ITGB4), a component of the focal adhesion complex. Silencing ITGB4 in tolerant cells improved sotorasib sensitivity, while overexpressing ITGB4 enhanced tolerance to sotorasib by supporting AKT-mTOR bypass signaling. Chronic treatment with sotorasib induced WNT expression and activated the WNT/β-catenin signaling pathway. Thus, silencing both ITGB4 and β-catenin significantly improved sotorasib sensitivity in tolerant, acquired, and inherently resistant cells. In addition, the proteasome inhibitor carfilzomib (CFZ) exhibited synergism with sotorasib by down-regulating ITGB4 and β-catenin expression. Furthermore, adagrasib phenocopies the combination effect of sotorasib and CFZ by suppressing KRAS activity and inhibiting cell cycle progression in inherently resistant cells. Overall, our findings unveil previously unrecognized nongenetic mechanisms underlying resistance to sotorasib and propose a promising treatment strategy to overcome resistance.
    MeSH term(s) Humans ; Antiviral Agents ; beta Catenin/genetics ; Carcinoma, Non-Small-Cell Lung/drug therapy ; Carcinoma, Non-Small-Cell Lung/genetics ; Lung Neoplasms/drug therapy ; Lung Neoplasms/genetics ; Mutation ; Proto-Oncogene Proteins p21(ras)/genetics ; Drug Resistance, Neoplasm/genetics
    Chemical Substances Antiviral Agents ; beta Catenin ; KRAS protein, human ; Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2)
    Language English
    Publishing date 2023-10-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.ade3816
    Database MEDical Literature Analysis and Retrieval System OnLINE

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