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Article ; Online: Structural insights into SARS-CoV-2 main protease conformational plasticity.

Dehury, Budheswar / Mishra, Sarbani / Pati, Sanghamitra

2023 Volume 124, Issue 6, Page(s) 861–876

Abstract: The spread of different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants underscores the need for insights into the structural properties of its structural and non-structural proteins. The highly conserved homo-dimeric chymotrypsin- ... ...

Abstract	The spread of different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants underscores the need for insights into the structural properties of its structural and non-structural proteins. The highly conserved homo-dimeric chymotrypsin-like protease (3CL M
MeSH term(s)	Humans ; SARS-CoV-2 ; Protein Conformation ; COVID-19 ; Cysteine Endopeptidases/metabolism ; Molecular Dynamics Simulation ; Protease Inhibitors/chemistry ; Molecular Docking Simulation ; Antiviral Agents/chemistry
Chemical Substances	3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Protease Inhibitors ; Antiviral Agents
Language	English
Publishing date	2023-04-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	392402-6
ISSN	1097-4644 ; 0730-2312
ISSN (online)	1097-4644
ISSN	0730-2312
DOI	10.1002/jcb.30409
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Article ; Online: Computational study on Schiff base derived salicylaldehyde and furfuraldehyde derivatives as potent anti-tubercular agents: prospect to dihydropteroate synthase inhibitors.

Sahoo, Chita Ranjan / Paidesetty, Sudhir Kumar / Dehury, Budheswar / Padhy, Rabindra Nath

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 5, Page(s) 2539–2549

Abstract: Nowadays, bacterial multidrug resistance has become a commonplace problem in clinics due to several intrinsic factors mediated through resistance to antibacterials ... ...

Abstract	Nowadays, bacterial multidrug resistance has become a commonplace problem in clinics due to several intrinsic factors mediated through resistance to antibacterials obtained
MeSH term(s)	Humans ; Dihydropteroate Synthase ; Schiff Bases/pharmacology ; Schiff Bases/chemistry ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/chemistry ; Aldehydes/pharmacology ; Aldehydes/chemistry ; Bacteria ; Antitubercular Agents/pharmacology ; Microbial Sensitivity Tests
Chemical Substances	salicylaldehyde (17K64GZH20) ; Dihydropteroate Synthase (EC 2.5.1.15) ; Schiff Bases ; Anti-Bacterial Agents ; Aldehydes ; Antitubercular Agents
Language	English
Publishing date	2023-05-30
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2217918
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Article ; Online: Molecular docking and MD simulations reveal protease inhibitors block the catalytic residues in Prp8 intein of

Panda, Sunita / Rout, Madhusmita / Mishra, Sarbani / Turuk, Jyotirmayee / Pati, Sanghamitra / Dehury, Budheswar

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–16

Abstract: Resistance to azoles and amphotericin B especially ... ...

Abstract	Resistance to azoles and amphotericin B especially in
Language	English
Publishing date	2023-12-27
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2298735
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Article ; Online: NMR insights into β-Lactamase activity of UVI31+ Protein from Chlamydomonas reinhardtii.

Rout, Ashok K / Gautam, Saurabh / Kumar Mishra, Vipin / Bopardikar, Mandar / Dehury, Budheswar / Singh, Himanshu

Journal of magnetic resonance (San Diego, Calif. : 1997)

2024 Volume 362, Page(s) 107689

Abstract: β-Lactamases (EC 3.5.2.6) confer resistance against β-lactam group-containing antibiotics in bacteria and higher eukaryotes, including humans. Pathogenic bacterial resistance against β-lactam antibiotics is a primary concern for potential therapeutic ... ...

Abstract	β-Lactamases (EC 3.5.2.6) confer resistance against β-lactam group-containing antibiotics in bacteria and higher eukaryotes, including humans. Pathogenic bacterial resistance against β-lactam antibiotics is a primary concern for potential therapeutic developments and drug targets. Here, we report putative β-lactamase activity, sulbactam binding (a β-lactam analogue) in the low μM affinity range, and site-specific interaction studies of a 14 kDa UV- and dark-inducible protein (abbreviated as UVI31+, a BolA homologue) from Chlamydomonas reinhartii. Intriguingly, the solution NMR structure of UVI31 + bears no resemblance to other known β-lactamases; however, the sulbactam binding is found at two sites rich in positively charged residues, mainly at the L2 loop regions and the N-terminus. Using NMR spectroscopy, ITC and MD simulations, we map the ligand binding sites in UVI31 + providing atomic-level insights into its β-lactamase activity. Current study is the first report on β-lactamase activity of UVI31+, a BolA analogue, from C. reinhartii. Furthermore, our mutation studies reveal that the active site serine-55 is crucial for β-lactamase activity.
Language	English
Publishing date	2024-04-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	1469665-4
ISSN	1096-0856 ; 1557-8968 ; 1090-7807 ; 0022-2364
ISSN (online)	1096-0856 ; 1557-8968
ISSN	1090-7807 ; 0022-2364
DOI	10.1016/j.jmr.2024.107689
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Article ; Online: Lipid and cholesterols modulate the dynamics of SARS-CoV-2 viral ion channel ORF3a and its pathogenic variants.

Rout, Madhusmita / Mishra, Sarbani / Panda, Sunita / Dehury, Budheswar / Pati, Sanghamitra

International journal of biological macromolecules

2023 Volume 254, Issue Pt 3, Page(s) 127986

Abstract: SARS-CoV-2 accessory protein, ORF3a is a putative ion channel which immensely contributes to viral pathogenicity by modulating host immune responses and virus-host interactions. Relatively high expression of ORF3a in diseased individuals and implication ... ...

Abstract	SARS-CoV-2 accessory protein, ORF3a is a putative ion channel which immensely contributes to viral pathogenicity by modulating host immune responses and virus-host interactions. Relatively high expression of ORF3a in diseased individuals and implication with inflammasome activation, apoptosis and autophagy inhibition, ratifies as an effective target for developing vaccines and therapeutics. Herein, we present the elusive dynamics of ORF3a-dimeric state using all-atoms molecular dynamics (MD) simulations at μ-seconds scale in a heterogeneous lipid-mimetic system in multiple replicates. Additionally, we also explore the effect of non-synonymous pathogenic mutations on ORF3a ion channel activity and viral pathogenicity in different SARS-CoV-2 variants using various structure-based protein stability (ΔΔG) tools and computational saturation mutagenesis. Our study ascertains the role of phosphatidylcholines and cholesterol in modulating the structure of ORF3a, which perturbs the size and flexibility of the polar cavity that allows permeation of large cations. Discrete trend in ion channel pore radius and area per lipid arises the premise that presence of lipids might also affect the overall conformation of ORF3a. MD structural-ensembles, in some replicates rationalize the crucial role of TM2 in maintaining the native structure of ORF3a. We also infer that loss of structural stability primarily grounds for pathogenicity in more than half of the pathogenic variants of ORF3a. Overall, the effect of mutation on alteration of ion permeability of ORF3a, proposed in this study brings mechanistic insights into variant consequences on viral membrane proteins of SARS-CoV-2, which can be utilized for the development of novel therapeutics to treat COVID-19 and other coronavirus diseases.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/genetics ; Ion Channels ; Cholesterol
Chemical Substances	Ion Channels ; Cholesterol (97C5T2UQ7J)
Language	English
Publishing date	2023-11-08
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.127986
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Article ; Online: Computational saturation mutagenesis to explore the effect of pathogenic mutations on extra-cellular domains of TREM2 associated with Alzheimer's and Nasu-Hakola disease.

Swain, Preety Sthutika / Panda, Sunita / Pati, Sanghamitra / Dehury, Budheswar

Journal of molecular modeling

2023 Volume 29, Issue 11, Page(s) 360

Abstract: Context: The specialised family of triggering receptors expressed on myeloid cells (TREMs) plays a pivotal role in causing neurodegenerative disorders and activating microglial anti-inflammatory responses. Nasu-Hakola disease (NHD), a rare autosomal ... ...

Abstract	Context: The specialised family of triggering receptors expressed on myeloid cells (TREMs) plays a pivotal role in causing neurodegenerative disorders and activating microglial anti-inflammatory responses. Nasu-Hakola disease (NHD), a rare autosomal recessive disorder, has been associated with mutations in TREM2, which is also responsible for raising the risk of Alzheimer's disease (AD). Herein, we have made an endeavour to differentiate the confirmed pathogenic variants in TREM2 extra-cellular domain (ECD) linked with NHD and AD using mutation-induced fold stability change (∆∆G), with the computation of 12distinct structure-based methods through saturation mutagenesis. Correlation analysis between relative solvent accessibility (RSA) and ∆∆G expresses the discrete distributive behaviour of mutants associated with TREM2 in AD (R Methods: ConSurf algorithm and ENDscript were used to determine the position and conservation of each residue in the wild-type ECD of TREM2. The mutation-induced fold stability change (∆∆G) of confirmed pathogenic mutants associated with NHD and AD was estimated using 12 state-of-the-art structure-based protein stability tools. Furthermore, we also computed the effect of random mutation on these sites using computational saturation mutagenesis. Linear regression analysis was performed using mutants ∆∆G and RSA through GraphPad software. In addition, a comprehensive non-bonded residual interaction network (RIN) of wild type and its mutants of TREM2-ECD was enumerated using RING3.0.
MeSH term(s)	Humans ; Alzheimer Disease/genetics ; Ligands ; Mutation ; Mutagenesis ; Membrane Glycoproteins/genetics ; Receptors, Immunologic/genetics
Chemical Substances	Ligands ; TREM2 protein, human ; Membrane Glycoproteins ; Receptors, Immunologic
Language	English
Publishing date	2023-11-04
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-023-05770-7
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Article ; Online: Spectroscopic insights with molecular docking and molecular dynamic simulation studies of anticancer drug 5-Fluorouracil targeting human pyruvate kinase m2.

Priyadarshinee, Mamali / Dehury, Budheswar / Mishra, Sarbani / Jena, Chitranjali / Patra, Manaswini / Mishra, Neeraj K / Samanta, Luna / Mallick, Bairagi C

Journal of biomolecular structure & dynamics

2024 , Page(s) 1–13

Abstract: This study was conducted to test the efficacy of 5-fluorouracil (5-FU) as an anticancer drug against the human pyruvate kinase isozyme M2 (PKM2) using spectroscopic, molecular docking and molecular dynamic simulation studies. PKM2 fluorescence quenching ... ...

Abstract	This study was conducted to test the efficacy of 5-fluorouracil (5-FU) as an anticancer drug against the human pyruvate kinase isozyme M2 (PKM2) using spectroscopic, molecular docking and molecular dynamic simulation studies. PKM2 fluorescence quenching studies in the presence of 5-FU performed at three different temperatures indicates dynamic quenching processes with single-set of binding (
Language	English
Publishing date	2024-02-12
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2024.2313158
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Article ; Online: All-atoms molecular dynamics study to screen potent efflux pump inhibitors against KpnE protein of

Dey, Suchanda / Rout, Madhusmita / Pati, Sanghamitra / Singh, Mahender Kumar / Dehury, Budheswar / Subudhi, Enketeswara

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 7, Page(s) 3492–3506

Abstract: The Small Multidrug Resistance efflux pump protein KpnE, plays a pivotal role in multi-drug resistance ... ...

Abstract	The Small Multidrug Resistance efflux pump protein KpnE, plays a pivotal role in multi-drug resistance in
MeSH term(s)	Molecular Dynamics Simulation ; Klebsiella pneumoniae ; Molecular Docking Simulation ; Escherichia coli/metabolism ; Lipid Bilayers/chemistry ; Antiporters/metabolism ; Escherichia coli Proteins/metabolism
Chemical Substances	Lipid Bilayers ; EmrE protein, E coli (147995-06-0) ; Antiporters ; Escherichia coli Proteins
Language	English
Publishing date	2023-05-22
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2214232
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Article ; Online: Membrane dynamics of γ-secretase with the anterior pharynx-defective 1B subunit.

Dehury, Budheswar / Kepp, Kasper P

Journal of cellular biochemistry

2020 Volume 122, Issue 1, Page(s) 69–85

Abstract: The four-subunit protease complex γ-secretase cleaves many single-pass transmembrane (TM) substrates, including Notch and β-amyloid precursor protein to generate amyloid-β (Aβ), central to Alzheimer's disease. Two of the subunits anterior pharynx- ... ...

Abstract	The four-subunit protease complex γ-secretase cleaves many single-pass transmembrane (TM) substrates, including Notch and β-amyloid precursor protein to generate amyloid-β (Aβ), central to Alzheimer's disease. Two of the subunits anterior pharynx-defective 1 (APH-1) and presenilin (PS) exist in two homologous forms APH1-A and APH1-B, and PS1 and PS2. The consequences of these variations are poorly understood and could affect Aβ production and γ-secretase medicine. Here, we developed the first complete structural model of the APH-1B subunit using the published cryo-electron microscopy (cryo-EM) structures of APH1-A (Protein Data Bank: 5FN2, 5A63, and 6IYC). We then performed all-atom molecular dynamics simulations at 303 K in a realistic bilayer system to understand both APH-1B alone and in γ-secretase without and with substrate C83-bound. We show that APH-1B adopts a 7TM topology with a water channel topology similar to APH-1A. We demonstrate direct transport of water through this channel, mainly via Glu84, Arg87, His170, and His196. The apo and holo states closely resemble the experimental cryo-EM structures with APH-1A, however with subtle differences: The substrate-bound APH-1B γ-secretase was quite stable, but some TM helices of PS1 and APH-1B rearranged in the membrane consistent with the disorder seen in the cryo-EM data. This produces different accessibility of water molecules for the catalytic aspartates of PS1, critical for Aβ production. In particular, we find that the typical distance between the catalytic aspartates of PS1 and the C83 cleavage sites are shorter in APH-1B, that is, it represents a more closed state, due to interactions with the C-terminal fragment of PS1. Our structural-dynamic model of APH-1B alone and in γ-secretase suggests generally similar topology but some notable differences in water accessibility which may be relevant to the protein's existence in two forms and their specific function and location.
Language	English
Publishing date	2020-08-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	392402-6
ISSN	1097-4644 ; 0730-2312
ISSN (online)	1097-4644
ISSN	0730-2312
DOI	10.1002/jcb.29832
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Article ; Online: Dissecting the Molecular Basis of Host Leucine-Rich Repeat Containing 15 Mediated Interaction with Receptor Binding Domain of SARS-CoV-2 Spike Protein: A Computational Approach.

Mishra, Sarbani / Sharma, Mansi / Singh, Mahendra Kumar / Pati, Sanghamitra / Dehury, Budheswar

The journal of physical chemistry letters

2023 Volume 14, Issue 40, Page(s) 8994–9001

Abstract: The detection of leucine-rich repeat containing 15 (LRRC15) as a connecting link with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the possibility of its involvement in differential restriction activity of SARS-CoV-2 pathways. ...

Abstract	The detection of leucine-rich repeat containing 15 (LRRC15) as a connecting link with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the possibility of its involvement in differential restriction activity of SARS-CoV-2 pathways. However, the structure-function mechanism of LRRC15 involving the receptor binding domain (RBD) of the SARS-CoV-2 spike protein and their mode of interaction is largely unknown. Using state-of-the-art AlphaFold2 and all-atom molecular dynamics simulations, our findings provide evidences of alternative binding modes of RBD with LRR units of LRRC15 having varied affinities. Contribution of both the receptor binding regions in RBD, including receptor binding motif in accommodating the LRR domain, towards the C-terminal region, emphasizes its differential role in modulating host cell receptiveness for SARS-CoV-2, the innate immune system, as well as antiviral tone. However, further experimental validations are necessary for unravelling the unknown mechanism and distinctive features of this host receptor in the COVID-19 pandemic, involving both the transmembrane as well as cytoplasmic domain.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2/metabolism ; Spike Glycoprotein, Coronavirus/chemistry ; Leucine ; Pandemics ; Angiotensin-Converting Enzyme 2/metabolism ; Protein Binding ; Molecular Dynamics Simulation ; Membrane Proteins/metabolism
Chemical Substances	spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Leucine (GMW67QNF9C) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; LRRC15 protein, human ; Membrane Proteins
Language	English
Publishing date	2023-10-02
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.3c01443
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