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  1. Article ; Online: Current biomarkers and treatment strategies in Alzheimer disease: An overview and future perspectives.

    Bhole, Ritesh P / Chikhale, Rupesh V / Rathi, Karishma M

    IBRO neuroscience reports

    2023  Volume 16, Page(s) 8–42

    Abstract: Alzheimer's disease (AD), a progressive degenerative disorder first identified by Alois Alzheimer in 1907, poses a significant public health challenge. Despite its prevalence and impact, there is currently no definitive ante mortem diagnosis for AD ... ...

    Abstract Alzheimer's disease (AD), a progressive degenerative disorder first identified by Alois Alzheimer in 1907, poses a significant public health challenge. Despite its prevalence and impact, there is currently no definitive ante mortem diagnosis for AD pathogenesis. By 2050, the United States may face a staggering 13.8 million AD patients. This review provides a concise summary of current AD biomarkers, available treatments, and potential future therapeutic approaches. The review begins by outlining existing drug targets and mechanisms in AD, along with a discussion of current treatment options. We explore various approaches targeting Amyloid β (Aβ), Tau Protein aggregation, Tau Kinases, Glycogen Synthase kinase-3β, CDK-5 inhibitors, Heat Shock Proteins (HSP), oxidative stress, inflammation, metals, Apolipoprotein E (ApoE) modulators, and Notch signaling. Additionally, we examine the historical use of Estradiol (E2) as an AD therapy, as well as the outcomes of Randomized Controlled Trials (RCTs) that evaluated antioxidants (e.g., vitamin E) and omega-3 polyunsaturated fatty acids as alternative treatment options. Notably, positive effects of docosahexaenoic acid nutriment in older adults with cognitive impairment or AD are highlighted. Furthermore, this review offers insights into ongoing clinical trials and potential therapies, shedding light on the dynamic research landscape in AD treatment.
    Language English
    Publishing date 2023-11-30
    Publishing country Netherlands
    Document type Journal Article ; Review
    ISSN 2667-2421
    ISSN (online) 2667-2421
    DOI 10.1016/j.ibneur.2023.11.003
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  2. Article ; Online: Evolution and Impact of Nucleic Acid Amplification Test (NAAT) for Diagnosis of Coronavirus Disease.

    Khan, Sumbul Fatma / Rathod, Priyanka / Gupta, Vivek K / Khedekar, Pramod B / Chikhale, Rupesh V

    Analytical chemistry

    2024  

    Language English
    Publishing date 2024-04-30
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.3c05225
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    Zs.A 4033: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Identification of novel hit molecules targeting M. tuberculosis polyketide synthase 13 by combining generative AI and physics-based methods.

    Chikhale, Rupesh V / Choudhary, Rinku / Malhotra, Jagriti / Eldesoky, Gaber E / Mangal, Parth / Patil, Pritee Chunarkar

    Computers in biology and medicine

    2024  Volume 176, Page(s) 108573

    Abstract: In this work we investigated the Pks13-TE domain, which plays a critical role in the viability of the mycobacteria. In this report, we have used a series of AI and Physics-based tools to identify Pks13-TE inhibitors. The Reinvent 4, pKCSM, KDeep, and ... ...

    Abstract In this work we investigated the Pks13-TE domain, which plays a critical role in the viability of the mycobacteria. In this report, we have used a series of AI and Physics-based tools to identify Pks13-TE inhibitors. The Reinvent 4, pKCSM, KDeep, and SwissADME are AI-ML-based tools. AutoDock Vina, PLANTS, MDS, and MM-GBSA are physics-based methods. A combination of these methods yields powerful support in the drug discovery cycle. Known inhibitors of Pks13-TE were collected, curated, and used as input for the AI-based tools, and Mol2Mol molecular optimisation methods generated novel inhibitors. These ligands were filtered based on physics-based methods like molecular docking and molecular dynamics using multiple tools for consensus generation. Rigorous analysis was performed on the selected compounds to reduce the chemical space while retaining the most promising compounds. The molecule interactions, stability of the protein-ligand complexes and the comparable binding energies with the native ligand were essential factors for narrowing the ligands set. The filtered ligands from docking, MDS, and binding energy colocations were further tested for their ADMET properties since they are among the essential criteria for this series of molecules. It was found that ligands Mt1 to Mt6 have excellent predicted pharmacokinetic, pharmacodynamic and toxicity profiles and good synthesisability.
    Language English
    Publishing date 2024-05-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2024.108573
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    Zs.A 653: Show issues Location:
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  4. Article: Editorial: Traditional medicine bioactives for management of diabetes mellitus.

    Khanal, Pukar / Chikhale, Rupesh / Dey, Yadu Nandan / Kazeem, Mutiu Idowu

    Frontiers in pharmacology

    2023  Volume 14, Page(s) 1205939

    Language English
    Publishing date 2023-06-06
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2587355-6
    ISSN 1663-9812
    ISSN 1663-9812
    DOI 10.3389/fphar.2023.1205939
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  5. Article ; Online: A Review on Five and Six-Membered Heterocyclic Compounds Targeting the Penicillin-Binding Protein 2 (PBP2A) of Methicillin-Resistant

    Ambade, Shraddha S / Gupta, Vivek Kumar / Bhole, Ritesh P / Khedekar, Pramod B / Chikhale, Rupesh V

    Molecules (Basel, Switzerland)

    2023  Volume 28, Issue 20

    Abstract: Staphylococcus ... ...

    Abstract Staphylococcus aureus
    MeSH term(s) Humans ; Penicillin-Binding Proteins/chemistry ; Methicillin-Resistant Staphylococcus aureus/metabolism ; Methicillin/metabolism ; Methicillin/pharmacology ; Staphylococcus aureus/metabolism ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/metabolism ; Monobactams/metabolism ; Bacterial Proteins/chemistry ; Microbial Sensitivity Tests
    Chemical Substances Penicillin-Binding Proteins ; Methicillin (Q91FH1328A) ; Anti-Bacterial Agents ; Monobactams ; Bacterial Proteins
    Language English
    Publishing date 2023-10-10
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules28207008
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    Zs.MO 81: Show issues

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  6. Article ; Online: Targeting dormant phenotype acquired mycobacteria using natural products by exploring its important targets:

    Sharma, Shweta / Chikhale, Rupesh / Shinde, Nivedita / Khan, A M / Gupta, Vivek Kumar

    Frontiers in cellular and infection microbiology

    2023  Volume 13, Page(s) 1111997

    Abstract: The dormant phenotype ... ...

    Abstract The dormant phenotype of
    MeSH term(s) Biological Products/pharmacology ; Biological Products/metabolism ; Molecular Docking Simulation ; Mycobacterium tuberculosis/metabolism ; Phenotype ; Molecular Dynamics Simulation
    Chemical Substances Biological Products
    Language English
    Publishing date 2023-03-24
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2023.1111997
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  7. Article: Identification of Mycobacterium tuberculosis transcriptional repressor EthR inhibitors: Shape-based search and machine learning studies.

    Chikhale, Rupesh V / Eldesoky, Gaber E / Kolpe, Mahima Sudhir / Suryawanshi, Vikramsinh Sardarsinh / Patil, Pritee Chunarkar / Bhowmick, Shovonlal

    Heliyon

    2024  Volume 10, Issue 5, Page(s) e26802

    Abstract: Tuberculosis has been a challenge to the world since prehistoric times, and with the advent of drug-resistant strains, it has become more challenging to treat this infection. Ethionamide (ETH), a second-line drug, acts as a prodrug and targets mycolic ... ...

    Abstract Tuberculosis has been a challenge to the world since prehistoric times, and with the advent of drug-resistant strains, it has become more challenging to treat this infection. Ethionamide (ETH), a second-line drug, acts as a prodrug and targets mycolic acid synthesis by targeting the enoyl-acyl carrier protein reductase (InhA) enzyme.
    Language English
    Publishing date 2024-02-22
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2024.e26802
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  8. Article ; Online: Machine learning assisted methods for the identification of low toxicity inhibitors of Enoyl-Acyl Carrier Protein Reductase (InhA).

    Chikhale, Rupesh V / Abdelghani, Heba Taha M / Deka, Hemchandra / Pawar, Atul Darasing / Patil, Pritee Chunarkar / Bhowmick, Shovonlal

    Computational biology and chemistry

    2024  Volume 110, Page(s) 108034

    Abstract: Tuberculosis (TB) is one of the life-threatening infectious diseases with prehistoric origins and occurs in almost all habitable parts of the world. TB mainly affects the lungs, and its etiological agent is Mycobacterium tuberculosis (Mtb). In 2022, more ...

    Abstract Tuberculosis (TB) is one of the life-threatening infectious diseases with prehistoric origins and occurs in almost all habitable parts of the world. TB mainly affects the lungs, and its etiological agent is Mycobacterium tuberculosis (Mtb). In 2022, more than 10 million people were infected worldwide, and 1.3 million were children. The current study considered the in-silico and machine learning (ML) approaches to explore the potential anti-TB molecules from the SelleckChem database against Enoyl-Acyl Carrier Protein Reductase (InhA). Initially, the entire database of ∼ 119000 molecules was sorted out through drug-likeness. Further, the molecular docking study was conducted to reduce the chemical space. The standard TB drug molecule's binding energy was considered a threshold, and molecules found with lower affinity were removed for further analyses. Finally, the molecules were checked for the pharmacokinetic and toxicity studies, and compounds found to have acceptable pharmacokinetic parameters and were non-toxic were considered as final promising molecules for InhA. The above approach further evaluated five molecules for ML-based toxicity and synthetic accessibility assessment. Not a single molecule was found toxic and each of them was revealed as easy to synthesise. The complex between InhA and proposed and standard molecules was considered for molecular dynamics simulation. Several statistical parameters showed the stability between InhA and the proposed molecule. The high binding affinity was also found for each of the molecules towards InhA using the MM-GBSA approach. Hence, the above approaches and findings exposed the potentiality of the proposed molecules against InhA.
    Language English
    Publishing date 2024-02-20
    Publishing country England
    Document type Journal Article
    ISSN 1476-928X
    ISSN (online) 1476-928X
    DOI 10.1016/j.compbiolchem.2024.108034
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  9. Article ; Online: Mycobacterial Membrane Protein Large 3 (MmpL3) Inhibitors: A Promising Approach to Combat Tuberculosis.

    Umare, Mohit D / Khedekar, Pramod B / Chikhale, Rupesh V

    ChemMedChem

    2021  Volume 16, Issue 20, Page(s) 3136–3148

    Abstract: Tuberculosis is a prominent aliment throughout the world and a leading cause of mortality among infectious diseases. Drug development for multi-drug resistance and reducing the current therapy time is the top priority. Mycobacterial membrane protein ... ...

    Abstract Tuberculosis is a prominent aliment throughout the world and a leading cause of mortality among infectious diseases. Drug development for multi-drug resistance and reducing the current therapy time is the top priority. Mycobacterial membrane protein large 3 (MmpL3) is a promising target with high potential, however, it has not been explored to its greatest potential. It is a membrane transporter that translocates trehalose-monomycolate which is a precursor for the synthesis of mycolic acid that is essential for the synthesis of the bacterial cell wall and is pathogenic in nature. In this review, we have discussed the current development of MmpL3 inhibitors, different scaffolds, their derivatives, and their synthetic schemes and provide insight into the challenges in developing these inhibitors.
    MeSH term(s) Antitubercular Agents/chemistry ; Antitubercular Agents/pharmacology ; Bacterial Proteins/antagonists & inhibitors ; Bacterial Proteins/metabolism ; Humans ; Membrane Transport Proteins/metabolism ; Microbial Sensitivity Tests ; Molecular Structure ; Mycobacterium tuberculosis/drug effects ; Tuberculosis/drug therapy ; Tuberculosis/metabolism
    Chemical Substances Antitubercular Agents ; Bacterial Proteins ; Membrane Transport Proteins ; MmpL3 protein, Mycobacterium tuberculosis
    Language English
    Publishing date 2021-08-03
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 2218496-X
    ISSN 1860-7187 ; 1860-7179
    ISSN (online) 1860-7187
    ISSN 1860-7179
    DOI 10.1002/cmdc.202100359
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    Zs.A 6280: Show issues Location:
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  10. Article ; Online: Transmission of SARS-CoV-2 in South Asian countries: molecular evolutionary model based phylogenetic and mutation analysis.

    Maurya, Anand Prakash / Chikhale, Rupesh V / Pandey, Piyush

    Environmental sustainability (Singapore)

    2020  Volume 4, Issue 3, Page(s) 533–541

    Abstract: The on-going coronavirus disease 19 (COVID-19) pandemic has caused a very high number of infections and deaths around the globe. The absence of vaccine/drugs to counter COVID-19 has scrambled scientific communities to repurpose available medicines/ ... ...

    Abstract The on-going coronavirus disease 19 (COVID-19) pandemic has caused a very high number of infections and deaths around the globe. The absence of vaccine/drugs to counter COVID-19 has scrambled scientific communities to repurpose available medicines/vaccines. As the virus is known to mutate, using the whole genome sequences, the transmission dynamics and molecular evolutionary models were evaluated for South Asian countries to determine the evolutionary rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Phylogenetic analyses were done using the data available on National Center for Biotechnology Information (NCBI). Different nucleotide substitution models and molecular evolutionary models were analyzed to see how SARS-CoV-2 was transmitted in the populations. Models for the viral 'S' and 'N' protein from selected strains were constructed, validated, and analyzed to determine the mutations and discover the potential therapeutics against this deadly viral disease. We found that the Hasegawa-Kishino-Yano (HKY) nucleotide substitution model was the best model with the lowest Bayesian information criterion (BIC) scores. Molecular clock RelTime analysis showed the evolutionary rate of SARS-CoV-2 substitutions in the genome was at 95% confidence interval, and heterogeneity was observed. Several mutations in the viral S-protein were found with one in the receptor-binding domain concerning SARS-CoV-2/Wuhan-1/S-Protein. Nucleocapsid protein also showed mutations in the strains from India and Sri Lanka. Our analysis suggests that SARS-CoV-2 is evolving at a diverse rate. The mutation leading to substitution in the nucleotide sequence occurred in the genome during the transmission of COVID-19 among individuals in the South Asian countries.
    Language English
    Publishing date 2020-09-18
    Publishing country Singapore
    Document type Journal Article
    ISSN 2523-8922
    ISSN (online) 2523-8922
    DOI 10.1007/s42398-020-00123-z
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