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  1. Article: Collaborative Research in Critical Care Medicine: A Way Forward to High-impact Publications from India.

    Ravisankar, Natesh Prabu / Singh, Ritu / Gurjar, Mohan

    Indian journal of critical care medicine : peer-reviewed, official publication of Indian Society of Critical Care Medicine

    2023  Volume 27, Issue 12, Page(s) 869–870

    Abstract: How to cite this article: ...

    Abstract How to cite this article:
    Language English
    Publishing date 2023-03-23
    Publishing country India
    Document type Editorial
    ZDB-ID 2121263-6
    ISSN 1998-359X ; 0972-5229
    ISSN (online) 1998-359X
    ISSN 0972-5229
    DOI 10.5005/jp-journals-10071-24614
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A Hybrid Docking and Machine Learning Approach to Enhance the Performance of Virtual Screening Carried out on Protein-Protein Interfaces.

    Singh, Natesh / Villoutreix, Bruno O

    International journal of molecular sciences

    2022  Volume 23, Issue 22

    Abstract: The modulation of protein-protein interactions (PPIs) by small chemical compounds is challenging. PPIs play a critical role in most cellular processes and are involved in numerous disease pathways. As such, novel strategies that assist the design of PPI ... ...

    Abstract The modulation of protein-protein interactions (PPIs) by small chemical compounds is challenging. PPIs play a critical role in most cellular processes and are involved in numerous disease pathways. As such, novel strategies that assist the design of PPI inhibitors are of major importance. We previously reported that the knowledge-based DLIGAND2 scoring tool was the best-rescoring function for improving receptor-based virtual screening (VS) performed with the Surflex docking engine applied to several PPI targets with experimentally known active and inactive compounds. Here, we extend our investigation by assessing the vs. potential of other types of scoring functions with an emphasis on docking-pose derived solvent accessible surface area (SASA) descriptors, with or without the use of machine learning (ML) classifiers. First, we explored rescoring strategies of Surflex-generated docking poses with five GOLD scoring functions (GoldScore, ChemScore, ASP, ChemPLP, ChemScore with Receptor Depth Scaling) and with consensus scoring. The top-ranked poses were post-processed to derive a set of protein and ligand SASA descriptors in the bound and unbound states, which were combined to derive descriptors of the docked protein-ligand complexes. Further, eight ML models (tree, bagged forest, random forest, Bayesian, support vector machine, logistic regression, neural network, and neural network with bagging) were trained using the derivatized SASA descriptors and validated on test sets. The results show that many SASA descriptors are better than Surflex and GOLD scoring functions in terms of overall performance and early recovery success on the used dataset. The ML models were superior to all scoring functions and rescoring approaches for most targets yielding up to a seven-fold increase in enrichment factors at 1% of the screened collections. In particular, the neural networks and random forest-based ML emerged as the best techniques for this PPI dataset, making them robust and attractive vs. tools for hit-finding efforts. The presented results suggest that exploring further docking-pose derived SASA descriptors could be valuable for structure-based virtual screening projects, and in the present case, to assist the rational design of small-molecule PPI inhibitors.
    MeSH term(s) Ligands ; Bayes Theorem ; Algorithms ; Proteins/chemistry ; Support Vector Machine
    Chemical Substances Ligands ; Proteins
    Language English
    Publishing date 2022-11-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms232214364
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  3. Article: Demystifying the Molecular Basis of Pyrazoloquinolinones Recognition at the Extracellular α1+/β3- Interface of the GABA

    Singh, Natesh / Villoutreix, Bruno O

    Frontiers in pharmacology

    2020  Volume 11, Page(s) 561834

    Abstract: ... ...

    Abstract GABA
    Keywords covid19
    Language English
    Publishing date 2020-09-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587355-6
    ISSN 1663-9812
    ISSN 1663-9812
    DOI 10.3389/fphar.2020.561834
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  4. Article: Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises.

    Singh, Natesh / Villoutreix, Bruno O

    Computational and structural biotechnology journal

    2021  Volume 19, Page(s) 2537–2548

    Abstract: There is an urgent need to identify new therapies that prevent SARS-CoV-2 infection and improve the outcome of COVID-19 patients. This pandemic has thus spurred intensive research in most scientific areas and in a short period of time, several vaccines ... ...

    Abstract There is an urgent need to identify new therapies that prevent SARS-CoV-2 infection and improve the outcome of COVID-19 patients. This pandemic has thus spurred intensive research in most scientific areas and in a short period of time, several vaccines have been developed. But, while the race to find vaccines for COVID-19 has dominated the headlines, other types of therapeutic agents are being developed. In this mini-review, we report several databases and online tools that could assist the discovery of anti-SARS-CoV-2 small chemical compounds and peptides. We then give examples of studies that combined in silico and in vitro screening, either for drug repositioning purposes or to search for novel bioactive compounds. Finally, we question the overall lack of discussion and plan observed in academic research in many countries during this crisis and suggest that there is room for improvement.
    Language English
    Publishing date 2021-04-26
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2021.04.059
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  5. Article ; Online: A toolkit for covalent docking with GOLD: from automated ligand preparation with KNIME to bound protein-ligand complexes.

    David, Laurianne / Mdahoma, Anissa / Singh, Natesh / Buchoux, Sébastien / Pihan, Emilie / Diaz, Constantino / Rabal, Obdulia

    Bioinformatics advances

    2022  Volume 2, Issue 1, Page(s) vbac090

    Abstract: Motivation: Current covalent docking tools have limitations that make them difficult to use for performing large-scale structure-based covalent virtual screening (VS). They require time-consuming tasks for the preparation of proteins and compounds ( ... ...

    Abstract Motivation: Current covalent docking tools have limitations that make them difficult to use for performing large-scale structure-based covalent virtual screening (VS). They require time-consuming tasks for the preparation of proteins and compounds (standardization, filtering according to the type of warheads), as well as for setting up covalent reactions. We have developed a toolkit to help accelerate drug discovery projects in the phases of hit identification by VS of ultra-large covalent libraries and hit expansion by exploration of the binding of known covalent compounds. With this application note, we offer the community a toolkit for performing automated covalent docking in a fast and efficient way.
    Results: The toolkit comprises a KNIME workflow for ligand preparation and a Python program to perform the covalent docking of ligands with the GOLD docking engine running in a parallelized fashion.
    Availability and implementation: The KNIME workflow entitled '
    Supplementary information: Supplementary data are available at
    Language English
    Publishing date 2022-11-29
    Publishing country England
    Document type Journal Article
    ISSN 2635-0041
    ISSN (online) 2635-0041
    DOI 10.1093/bioadv/vbac090
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  6. Article ; Online: Insights into the Structure, Function, and Ligand Discovery of the Large Neutral Amino Acid Transporter 1, LAT1

    Natesh Singh / Gerhard F. Ecker

    International Journal of Molecular Sciences, Vol 19, Iss 5, p

    2018  Volume 1278

    Abstract: The large neutral amino acid transporter 1 (LAT1, or SLC7A5) is a sodium- and pH-independent transporter, which supplies essential amino acids (e.g., leucine, phenylalanine) to cells. It plays an important role at the Blood–Brain Barrier (BBB) where it ... ...

    Abstract The large neutral amino acid transporter 1 (LAT1, or SLC7A5) is a sodium- and pH-independent transporter, which supplies essential amino acids (e.g., leucine, phenylalanine) to cells. It plays an important role at the Blood–Brain Barrier (BBB) where it facilitates the transport of thyroid hormones, pharmaceuticals (e.g., l-DOPA, gabapentin), and metabolites into the brain. Moreover, its expression is highly upregulated in various types of human cancer that are characterized by an intense demand for amino acids for growth and proliferation. Therefore, LAT1 is believed to be an important drug target for cancer treatment. With the crystallization of the arginine/agmatine antiporter (AdiC) from Escherichia Coli, numerous homology models of LAT1 have been built to elucidate the substrate binding site, ligand–transporter interaction, and structure–function relationship. The use of these models in combination with molecular docking and experimental testing has identified novel chemotypes of ligands of LAT1. Here, we highlight the structure, function, transport mechanism, and homology modeling of LAT1. Additionally, results from structure–function studies performed on LAT1 are addressed, which have enhanced our knowledge of the mechanism of substrate binding and translocation. This is followed by a discussion on ligand- and structure-based approaches, with an emphasis on elucidating the molecular basis of LAT1 inhibition. Finally, we provide an exhaustive summary of different LAT1 inhibitors that have been identified so far, including the recently discovered irreversible covalent inhibitors.
    Keywords amino acid transporter ; LAT1 ; AdiC ; anticancer ; melphalan ; covalent inhibitor ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 550
    Language English
    Publishing date 2018-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: Evaluation of Tools to Assess Symptoms and Symptom Severity in Patients With Medically Unexplained Physical Symptoms: A Systematic Review and Narrative Synthesis.

    Kuanar Baboo, Ananta Gopal / Ranjan, Piyush / Kaur, Tanveer / Rawat, Nandini / Sarkar, Siddharth / Kaloiya, Gaurishanker / Singh, Amandeep / Babu, Natesh / Baitha, Upendra / Prakash, Bindu

    Cureus

    2024  Volume 16, Issue 3, Page(s) e56204

    Abstract: A substantial portion of patients presenting to healthcare settings exhibit physical symptoms lacking clear, demonstrable organic causes. Accurate assessment of symptom severity is crucial for documenting outcomes and establishing treatment efficacy. ... ...

    Abstract A substantial portion of patients presenting to healthcare settings exhibit physical symptoms lacking clear, demonstrable organic causes. Accurate assessment of symptom severity is crucial for documenting outcomes and establishing treatment efficacy. This systematic review and narrative synthesis aims to provide researchers with insights into available and validated tools for assessing medically unexplained physical symptoms (MUPS). It involved comprehensive searches across electronic databases, including PubMed, Wiley, and Cochrane, adhering to PRISMA and COSMIN guidelines. The study comprised two phases: Phase 1 systematically reviewed tools for assessing MUPS symptoms and severity, while Phase 2 conducted a narrative synthesis of their measurement properties, focusing on validity and reliability. Out of 14,459 records, 191 articles were identified, leading to the recognition of 16 validated tools for assessing MUPS symptoms and severity. Most tools demonstrated excellent internal consistency and structural validity. However, the majority lacked cross-cultural validity. The choice of tools for the assessment of MUPS will assist clinicians and researchers in determining the severity of MUPS and developing a tailored treatment plan to improve the physical and psychological functioning of these patients.
    Language English
    Publishing date 2024-03-15
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2747273-5
    ISSN 2168-8184
    ISSN 2168-8184
    DOI 10.7759/cureus.56204
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  8. Article ; Online: Insights into the Structure, Function, and Ligand Discovery of the Large Neutral Amino Acid Transporter 1, LAT1.

    Singh, Natesh / Ecker, Gerhard F

    International journal of molecular sciences

    2018  Volume 19, Issue 5

    Abstract: The large neutral amino acid transporter 1 (LAT1, or SLC7A5) is a sodium- and pH-independent transporter, which supplies essential amino acids (e.g., leucine, phenylalanine) to cells. It plays an important role at the Blood⁻Brain Barrier (BBB) where it ... ...

    Abstract The large neutral amino acid transporter 1 (LAT1, or SLC7A5) is a sodium- and pH-independent transporter, which supplies essential amino acids (e.g., leucine, phenylalanine) to cells. It plays an important role at the Blood⁻Brain Barrier (BBB) where it facilitates the transport of thyroid hormones, pharmaceuticals (e.g., l-DOPA, gabapentin), and metabolites into the brain. Moreover, its expression is highly upregulated in various types of human cancer that are characterized by an intense demand for amino acids for growth and proliferation. Therefore, LAT1 is believed to be an important drug target for cancer treatment. With the crystallization of the arginine/agmatine antiporter (AdiC) from
    MeSH term(s) Binding Sites ; Drug Discovery ; Humans ; Large Neutral Amino Acid-Transporter 1/chemistry ; Large Neutral Amino Acid-Transporter 1/metabolism ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Prodrugs ; Protein Binding ; Structure-Activity Relationship
    Chemical Substances Large Neutral Amino Acid-Transporter 1 ; Ligands ; Prodrugs
    Language English
    Publishing date 2018-04-24
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms19051278
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Kinase signaling as a drug target modality for regulation of vascular hyperpermeability: A case for ARDS therapy development.

    Kayyali, Usamah S / Ghandakly, Elizabeth / Singh, Natesh / Villoutreix, Bruno O / Tsaioun, Katya

    Drug discovery today

    2022  Volume 27, Issue 5, Page(s) 1448–1456

    Abstract: The endothelial vascular permeability barrier has an important role throughout the body's extensive vasculature, and its disruption leads to vascular hyperpermeability (leakage), which is associated with numerous medical conditions. In the lung, vascular ...

    Abstract The endothelial vascular permeability barrier has an important role throughout the body's extensive vasculature, and its disruption leads to vascular hyperpermeability (leakage), which is associated with numerous medical conditions. In the lung, vascular hyperpermeability can lead to pulmonary edema and acute respiratory distress syndrome (ARDS), the most severe and deadly complication of viral and bacterial infections, trauma and radiation exposure. There is currently no pharmacological treatment for ARDS with the only approved options being focused on supportive care. The development of effective treatments for ARDS has a potential to turn infectious diseases such as bacterial and viral pneumonia (including COVID-19) into manageable conditions, saving lives and providing a new tool to combat future epidemics. Strategies that aim to protect and augment the vascular endothelial barrier are important avenues to consider as potential treatments for ARDS and other conditions underlined by vascular hyperpermeability. We propose the activation of the MAPKAPK2 (MK2) kinase pathway as a new approach to augment the endothelial barrier and prevent or reverse ARDS and other conditions characterized by vascular barrier dysfunction.
    MeSH term(s) COVID-19/drug therapy ; Capillary Permeability ; Humans ; Lung/metabolism ; Respiratory Distress Syndrome/drug therapy ; Signal Transduction
    Language English
    Publishing date 2022-01-24
    Publishing country England
    Document type Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1324988-5
    ISSN 1878-5832 ; 1359-6446
    ISSN (online) 1878-5832
    ISSN 1359-6446
    DOI 10.1016/j.drudis.2022.01.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: The first laminin G-like domain of protein S is essential for binding and activation of Tyro3 receptor and intracellular signalling.

    Al Kafri, Nour / Ahnström, Josefin / Teraz-Orosz, Adrienn / Chaput, Ludovic / Singh, Natesh / Villoutreix, Bruno O / Hafizi, Sassan

    Biochemistry and biophysics reports

    2022  Volume 30, Page(s) 101263

    Abstract: The homologous proteins Gas6 and protein S (ProS1) are both natural ligands for the TAM (Tyro3, Axl, MerTK) receptor tyrosine kinases. ProS1 selectively activates Tyro3; however, the precise molecular interface of the ProS1-Tyro3 contact has not been ... ...

    Abstract The homologous proteins Gas6 and protein S (ProS1) are both natural ligands for the TAM (Tyro3, Axl, MerTK) receptor tyrosine kinases. ProS1 selectively activates Tyro3; however, the precise molecular interface of the ProS1-Tyro3 contact has not been characterised. We used a set of chimeric proteins in which each of the
    Language English
    Publishing date 2022-04-28
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2831046-9
    ISSN 2405-5808 ; 2405-5808
    ISSN (online) 2405-5808
    ISSN 2405-5808
    DOI 10.1016/j.bbrep.2022.101263
    Database MEDical Literature Analysis and Retrieval System OnLINE

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