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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

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

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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
Database	MEDical Literature Analysis and Retrieval System OnLINE

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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
Database	MEDical Literature Analysis and Retrieval System OnLINE

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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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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
Database	MEDical Literature Analysis and Retrieval System OnLINE

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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

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Article ; Online: Breaking through resistance in mCRPC

Ritesh P. Bhole / Payal M. Karche / Shaliendra S. Gurav / Rupesh V. Chikhale

Results in Chemistry, Vol 6, Iss , Pp 101143- (2023)

Enzalutamide analogues as effective anticancer agents for enhanced male survival

2023

Abstract: To alleviate metastatic castration-resistant prostate cancer (mCRPC), enzalutamide, a non-steroidal antiandrogen, is employed. Following androgen deprivation therapy or anti-androgen treatment, compensatory mechanisms in prostate cancer have been ... ...

Abstract	To alleviate metastatic castration-resistant prostate cancer (mCRPC), enzalutamide, a non-steroidal antiandrogen, is employed. Following androgen deprivation therapy or anti-androgen treatment, compensatory mechanisms in prostate cancer have been identified, leading to increased expression and function of steroidal receptors. Comparative studies involving individuals with CRPC have demonstrated enzalutamide's superior efficacy compared to its predecessor, bicalutamide. Currently, there are four nonsteroidal antiandrogens approved by the US Food and Drug Administration, with two investigational medications undergoing clinical trials. Enzalutamide effectively slowed prostate cancer growth by preventing nuclear translocation and gene expression that are dependent on the AR, according to preclinical research. Its effectiveness in metastatic hormone-sensitive prostate cancer was supported by clinical trials like ARCHES, which also showed an improvement in radiographic progression-free survival with an acceptable safety profile. Resistance to enzalutamide can occur due to the F786L mutation. Recent research has shown that analogues of enzalutamide can overcome this resistance, enhancing anticancer activity and improving male survival rates. We will explore various enzalutamide analogues, including those with trifluoromethyl, trifluoromethoxy, diarylhydantoin, benzothiazole or benzoxazole, and 1-hydroxy-2,2,2-trifluoro-1-ethyl moieties, primarily used to address the resistance issue. Additionally, we will highlight the structural activity relationships of these analogues, which may enhance their antiproliferative effects and increase male survival rates. Notably, imidazolidine derivatives exhibit the most significant antiproliferative activity.
Keywords	Metastatic Castration Resistant prostate cancer ; Enzalutamide ; Nonsteroidal antiandrogens ; AR ; F786L mutation ; Chemistry ; QD1-999
Subject code	610
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of sugar-containing natural products that interact with i-motif DNA.

Chikhale, Rupesh V / Guneri, Dilek / Yuan, Robert / Morris, Christopher J / Waller, Zoë A E

Bioorganic & medicinal chemistry letters

2022 Volume 73, Page(s) 128886

Abstract: There are thousands of compounds shown to interact with G-quadruplex DNA, yet very few which target i-motif (iM) DNA. Previous work showed that tobramycin can interact with iM- DNA, indicating the potential for sugar-molecules to target these structures. ...

Abstract	There are thousands of compounds shown to interact with G-quadruplex DNA, yet very few which target i-motif (iM) DNA. Previous work showed that tobramycin can interact with iM- DNA, indicating the potential for sugar-molecules to target these structures. Computational approaches indicated that the sugar-containing natural products baicalin and geniposidic acid had potential to target iM-DNA. We assessed the DNA interacting properties of these compounds using FRET-based DNA melting and a fluorescence-based displacement assay using iM-DNA structures from the human telomere and the insulin linked polymorphic region (ILPR), as well as complementary G-quadruplex and double stranded DNA. Both baicalin and geniposidic acid show promise as iM-interacting compounds with potential for use in experiments into the structure and function of i-motif forming DNA sequences and present starting points for further synthetic development of these as probes for iM-DNA.
MeSH term(s)	Biological Products ; DNA/chemistry ; G-Quadruplexes ; Humans ; Nucleic Acid Denaturation ; Sugars
Chemical Substances	Biological Products ; Sugars ; DNA (9007-49-2)
Language	English
Publishing date	2022-07-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1063195-1
ISSN	1464-3405 ; 0960-894X
ISSN (online)	1464-3405
ISSN	0960-894X
DOI	10.1016/j.bmcl.2022.128886
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Zs.A 3203: Show issues

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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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Article ; Online: Mycobacterium enoyl acyl carrier protein reductase (InhA): A key target for antitubercular drug discovery.

Prasad, Mayuri S / Bhole, Ritesh P / Khedekar, Pramod B / Chikhale, Rupesh V

Bioorganic chemistry

2021 Volume 115, Page(s) 105242

Abstract: Enoyl acyl carrier protein reductase (InhA) is a key enzyme involved in fatty acid synthesis mainly mycolic acid biosynthesis that is a part of NADH dependent acyl carrier protein reductase family. The aim of the present literature is to underline the ... ...

Abstract	Enoyl acyl carrier protein reductase (InhA) is a key enzyme involved in fatty acid synthesis mainly mycolic acid biosynthesis that is a part of NADH dependent acyl carrier protein reductase family. The aim of the present literature is to underline the different scaffolds or enzyme inhibitors that inhibit mycolic acid biosynthesis mainly cell wall synthesis by inhibiting enzyme InhA. Various scaffolds were identified based on the screening technologies like high throughput screening, encoded library technology, fragment-based screening. The compounds studied include indirect inhibitors (Isoniazid, Ethionamide, Prothionamide) and direct inhibitors (Triclosan/Diphenyl ethers, Pyrrolidine Carboxamides, Pyrroles, Acetamides, Thiadiazoles, Triazoles) with better efficacy against drug resistance. Out of the several scaffolds studied, pyrrolidine carboxamides were found to be the best molecules targeting InhA having good bioavailability properties and better MIC. This review provides with a detailed information, analysis, structure activity relationship and useful insight on various scaffolds as InhA inhibitors.
MeSH term(s)	Antitubercular Agents/chemical synthesis ; Antitubercular Agents/chemistry ; Antitubercular Agents/pharmacology ; Dose-Response Relationship, Drug ; Drug Discovery ; Humans ; Inhibins/antagonists & inhibitors ; Inhibins/metabolism ; Microbial Sensitivity Tests ; Molecular Structure ; Mycobacterium tuberculosis/drug effects ; Structure-Activity Relationship
Chemical Substances	Antitubercular Agents ; inhibin-alpha subunit ; Inhibins (57285-09-3)
Language	English
Publishing date	2021-08-08
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	120080-x
ISSN	1090-2120 ; 0045-2068
ISSN (online)	1090-2120
ISSN	0045-2068
DOI	10.1016/j.bioorg.2021.105242
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