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Article ; Online: Breaking the 'don't eat me' signal: in silico design of CD47-directed peptides for cancer immunotherapy.

Laddha, Kapil / Sobhia, M Elizabeth

2023

Abstract: The leading cause of death worldwide is cancer. Although there are various therapies available to treat cancer, finding a successful one can be like searching for a needle in a haystack. Immunotherapy appears to be one of those needles in the haystack of ...

Abstract	The leading cause of death worldwide is cancer. Although there are various therapies available to treat cancer, finding a successful one can be like searching for a needle in a haystack. Immunotherapy appears to be one of those needles in the haystack of cancer treatment. Immunotherapeutic agents enhance the immune response of the patient's body to tumor cells. One of the immunotherapeutic targets, Cluster of Differentiation 47 (CD47), releases the "don't eat me" signal when it binds to its receptor, Signal Regulatory Protein (SIRPα). Tumor cells use this signal to circumvent the immune system, rendering it ineffective. To stop tumor cells from releasing the "don't eat me" signal, the CD47-SIRPα interaction is specifically targeted in this study. To do so, in silico peptides were designed based on the structural analysis of the interaction between two proteins using point mutations on the interacting residues with the other amino acids. The peptide library was designed and docked on SIRPα using computational tools. Later on, after analyzing the docked complex, the best of them was selected for MD simulation studies of 100 ns. Further analysis after MD studies was carried out to determine the possible potential anti-SIRPα peptides.
Language	English
Publishing date	2023-09-28
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-023-10732-5
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Article ; Online: Water network chemistry to exploit the nature of catalytic water molecules in

Kumar, G Siva / Sobhia, M Elizabeth

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 2, Page(s) 725–733

Abstract: The dynamics of DNA gyrase and mutants of DNA gyrA such as G88A, A90V, S91P, D94A, D94G, D94N, D94Y; and double-point mutant (S91P-D94G), are meticulously investigated using computational approaches. Molecular dynamics (MD) and hydration thermodynamics ... ...

Abstract	The dynamics of DNA gyrase and mutants of DNA gyrA such as G88A, A90V, S91P, D94A, D94G, D94N, D94Y; and double-point mutant (S91P-D94G), are meticulously investigated using computational approaches. Molecular dynamics (MD) and hydration thermodynamics have shed light on the fundamental, mechanistic basis of mutations on the conformational stability of Quinolone Binding Pocket (QBP) of DNA gyrase. Analysis of MD results revealed the displacement of a single crystal water molecule (HOH201) from the catalytic site of wild-type (WT) and mutants of DNA gyrA. This prompted our research group to probe the five crystal water molecules present in the QBP of the enzyme using water thermodynamics. Hydration thermodynamics analysis revealed the displacement of HOH201 due to unstable thermodynamic signatures. Further, the analysis highlighted significant changes in thermodynamic signatures and locations of five crystal water hydration sites upon mutation. Integrated MD simulations and water thermodynamics provided promising insights into the conformational changes and inaccessibility of the catalytic water molecule that can influence the design of DNA gyrase inhibitors.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Fluoroquinolones ; DNA Gyrase/chemistry ; Water ; Mycobacterium tuberculosis/genetics ; Microbial Sensitivity Tests ; Mutation ; DNA ; Drug Resistance, Bacterial/genetics
Chemical Substances	Fluoroquinolones ; DNA Gyrase (EC 5.99.1.3) ; Water (059QF0KO0R) ; DNA (9007-49-2)
Language	English
Publishing date	2023-04-25
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2199869
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Article ; Online: Bifunctional robots inducing targeted protein degradation.

Sobhia, M Elizabeth / Kumar, Harish / Kumari, Sonia

European journal of medicinal chemistry

2023 Volume 255, Page(s) 115384

Abstract: The gaining importance of Targeted Protein Degradation (TPD) and PROTACs (PROteolysis-TArgeting Chimeras) have drawn the scientific community's attention. PROTACs are considered bifunctional robots owing to their avidity for the protein of interest (POI) ...

Abstract	The gaining importance of Targeted Protein Degradation (TPD) and PROTACs (PROteolysis-TArgeting Chimeras) have drawn the scientific community's attention. PROTACs are considered bifunctional robots owing to their avidity for the protein of interest (POI) and E3-ligase, which induce the ubiquitination of POI. These molecules are based on event-driven pharmacology and are applicable in different conditions such as oncology, antiviral, neurodegenerative disease, acne etc., offering tremendous scope to researchers. In this review, primarily, we attempted to compile the recent works available in the literature on PROTACs for various targeted proteins. We summarized the design and development strategies with a focus on molecular information of protein residues and linker design. Rationalization of the ternary complex formation using Artificial Intelligence including machine & deep learning models and traditionally followed computational tools are also included in this study. Moreover, details describing the optimization of PROTACs chemistry and pharmacokinetic properties are added. Advanced PROTAC designs and targeting complex proteins, is summed up to cover the wide spectrum.
MeSH term(s)	Humans ; Proteolysis ; Artificial Intelligence ; Neurodegenerative Diseases ; Robotics ; Ubiquitin-Protein Ligases/metabolism ; Proteins/metabolism
Chemical Substances	Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Proteins
Language	English
Publishing date	2023-04-15
Publishing country	France
Document type	Journal Article ; Review
ZDB-ID	188597-2
ISSN	1768-3254 ; 0009-4374 ; 0223-5234
ISSN (online)	1768-3254
ISSN	0009-4374 ; 0223-5234
DOI	10.1016/j.ejmech.2023.115384
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Article ; Online: An

Mallick, Moyim / Yoithap Prabhunath, T R / Kumari, Sonia / Sobhia, M Elizabeth

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–11

Abstract: Ameloblastoma is a benign odontogenic jawbone tumor. The binding of Nerve growth factor (NGF) to receptor tyrosine kinase A (TrkA) promotes cell survival, proliferation, and ... ...

Abstract	Ameloblastoma is a benign odontogenic jawbone tumor. The binding of Nerve growth factor (NGF) to receptor tyrosine kinase A (TrkA) promotes cell survival, proliferation, and differentiation
Language	English
Publishing date	2023-11-17
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2278083
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Article ; Online: Rational design of FXR agonists: a computational approach for NASH therapy.

Gandhe, Akshata / Kumari, Sonia / Elizabeth Sobhia, Masilamani

Molecular diversity

2023

Abstract: Non-alcoholic fatty liver disease (NAFLD) is a hepatic manifestation of the metabolic syndrome, posing risks to cardiovascular and hepatic health worldwide. Non-alcoholic steatohepatitis (NASH) which is a severe form of NAFLD, has a global prevalence. ... ...

Abstract	Non-alcoholic fatty liver disease (NAFLD) is a hepatic manifestation of the metabolic syndrome, posing risks to cardiovascular and hepatic health worldwide. Non-alcoholic steatohepatitis (NASH) which is a severe form of NAFLD, has a global prevalence. Therapeutic targets for NASH include THR-β, GLP-1 receptor, PPARα/δ/γ, FGF21 analogs, and FXR, a bile acid nuclear receptor pivotal for regulating bile acid synthesis and excretion. Our study aims to design the non-steroidal FXR agonist for NASH treatment, as FXR's role in the regulation of bile acid processes, rendering it a promising drug target for NASH therapy. Utilizing tropifexor as a reference molecule, we generated a shape-based pharmacophore model with seven features, identifying key binding requirements within the FXR active site. Virtual screening using this model, coupled with molecular docking studies, helped pinpoint potential ligands from diverse small molecule databases. Further analysis via MM/GBSA revealed 12 molecules with binding affinities comparable to tropifexor. Among them, DB15416 exhibited the lowest binding free energy and superior docking scores. To assess its dynamic stability, we subjected DB15416 to molecular dynamics simulations, confirming its suitability as a FXR agonist. These findings suggest that DB15416 holds promise as a FXR agonist for NASH treatment, which can be evaluated by experimental studies.
Language	English
Publishing date	2023-12-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-023-10766-9
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Article ; Online: Molecular dynamic assisted investigation on impact of mutations in deazaflavin dependent nitroreductase against pretomanid: a computational study.

Singh, Ravi / Shaheer, Muhammed / Sobhia, M Elizabeth

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 10, Page(s) 4421–4443

Abstract: In the past decade, TB drugs belonging to the nitroimidazole class, pretomanid and delamanid, have been authorised to treat MDR-TB and XDR-TB. With a novel inhibition mechanism and a reduction in the span of treatment, it is now being administered in ... ...

Abstract	In the past decade, TB drugs belonging to the nitroimidazole class, pretomanid and delamanid, have been authorised to treat MDR-TB and XDR-TB. With a novel inhibition mechanism and a reduction in the span of treatment, it is now being administered in various combinations. This approach is not the ultimate remedy since the target protein Deazaflavin dependent nitroreductase (Ddn) has a high mutation frequency, and already pretomanid resistant clinical isolates are reported in various studies. Ddn is essential for
MeSH term(s)	Molecular Dynamics Simulation ; Ligands ; Nitroimidazoles/pharmacology ; Nitroimidazoles/chemistry ; Nitroimidazoles/metabolism ; Mycobacterium tuberculosis/genetics ; Mutation ; Nitroreductases/genetics ; Nitroreductases/chemistry ; Nitroreductases/metabolism ; Antitubercular Agents/pharmacology
Chemical Substances	pretomanid ; Ligands ; Nitroimidazoles ; Nitroreductases (EC 1.7.-) ; Antitubercular Agents
Language	English
Publishing date	2022-05-14
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2069156
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Article ; Online: Identification of Potential ACE2-Derived Peptide Mimetics in SARS-CoV-2 Omicron Variant Therapeutics using Computational Approaches.

Paul, Stanly / Nadendla, Swathi / Sobhia, M Elizabeth

The journal of physical chemistry letters

2022 Volume 13, Issue 32, Page(s) 7420–7428

Abstract: The COVID-19 pandemic has become a global health challenge because of the emergence of distinct variants. Omicron, a new variant, is recognized as a variant of concern (VOC) by the World Health Organization (WHO) because of its higher mutations and ... ...

Abstract	The COVID-19 pandemic has become a global health challenge because of the emergence of distinct variants. Omicron, a new variant, is recognized as a variant of concern (VOC) by the World Health Organization (WHO) because of its higher mutations and accelerated human infection. The infection rate is strongly dependent on the binding rate of the receptor binding domain (RBD) against human angiotensin converting enzyme-2 (ACE2
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; Biomimetic Materials/therapeutic use ; Humans ; Mutation ; Pandemics ; Peptides/metabolism ; Peptidyl-Dipeptidase A/chemistry ; Protein Binding ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry ; COVID-19 Drug Treatment
Chemical Substances	Peptides ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-08-05
Publishing country	United States
Document type	Journal Article
ISSN	1948-7185
ISSN (online)	1948-7185
DOI	10.1021/acs.jpclett.2c01155
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Article ; Online: Identification of prospective covalent inhibitors for SARS-CoV-2 main protease using structure-based approach.

Gayatri, Shenvi Kudchadker / Chhabra, Vaishnavi / Kumar, Harish / Sobhia, M Elizabeth

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 16, Page(s) 7913–7930

Abstract: ... through mutation, develops into new variants of the virus that have appeared over time. As main protease (M ...

Abstract	The rapid global spread of SARS-CoV-2 has recently caused havoc and forced the world into a state of the pandemic causing respiratory, gastrointestinal, hepatic, and neurologic diseases. It persistently, through mutation, develops into new variants of the virus that have appeared over time. As main protease (M
Language	English
Publishing date	2022-10-06
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2129453
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Article ; Online: Protein degradation: a novel computational approach to design protein degrader probes for main protease of SARS-CoV-2.

Shaheer, Muhammed / Singh, Ravi / Sobhia, M Elizabeth

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 21, Page(s) 10905–10917

Abstract: ... insights on the design of suitable PROTACs for the main protease (M ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has afflicted many lives and led to approvals of drugs and vaccines for emergency use. Even though vaccines have emerged, the high mortality of COVID-19 and its insurgent proliferation throughout the masses commands an innovative therapeutic proposition for the treatment. Targeted protein degradation has been applied to various disease domains and we propose that it could be incredibly beneficial to tackle the current pandemic. In this study, we have attempted to furnish insights on the design of suitable PROTACs for the main protease (M
MeSH term(s)	Humans ; SARS-CoV-2/metabolism ; Coronavirus 3C Proteases/metabolism ; COVID-19 ; Proteolysis ; Protease Inhibitors/pharmacology ; Viral Nonstructural Proteins/metabolism ; Molecular Docking Simulation ; Cysteine Endopeptidases ; Antiviral Agents/pharmacology ; Molecular Dynamics Simulation
Chemical Substances	Coronavirus 3C Proteases (EC 3.4.22.28) ; Protease Inhibitors ; Viral Nonstructural Proteins ; Cysteine Endopeptidases (EC 3.4.22.-) ; Antiviral Agents
Language	English
Publishing date	2021-07-30
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1953601
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Article ; Online: Design and development of potent h-ACE2 derived peptide mimetics in SARS-CoV-2 Omicron variant therapeutics

Paul, Stanly M L / Nadendla, Swathi / Sobhia, Elizabeth M

bioRxiv

Abstract: The pandemic of COVID- 19 has become the global health challenge due to the emergence of new variants. The Receptor binding domain (RBD) of spike protein that makes direct interaction with ACE-2 has shown unique mutated residues in most of the variants ... ...

Abstract	The pandemic of COVID- 19 has become the global health challenge due to the emergence of new variants. The Receptor binding domain (RBD) of spike protein that makes direct interaction with ACE-2 has shown unique mutated residues in most of the variants of concern (VOC). Recently WHO declared the Omicron (B.1.1.529) as VOC considering it as a highly mutated variant which includes a total of 60 mutations out of which 15 mutations occurred in RBD region of SARS-CoV-2. Inhibition of Protein-protein (Omicron RBD-h-ACE2) interaction was already proved to inhibit the viral infection. In this study, by using molecular dynamic simulations efforts are made to explore the atomistic details of Omicron RBD-h-ACE2 interaction. Based on MD simulations, h-ACE2 motif is found to be interacting with omicron RBD domain. Interaction analysis had provided key residues interacting with Omicron-RBD that helped to extract h-ACE2 peptide. Here, rational design of the peptides that have resemblance with h-ACE2 is done and the peptide library is subjected for inhibition studies against Omicron-RBD. The current study helped to identify the significant peptides that can inhibit Omicron-RBD. Altogether the performed studies will provide an opportunity to develop potential therapeutic peptidomimetics effective against Omicron variant of SARS-CoV-2.
Keywords	covid19
Language	English
Publishing date	2022-02-02
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.02.01.478632
Database	COVID19

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