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Mirsadeghi FA, Rufchahi EM, Zarrabi S. Spectral characterization and computational studies of some new synthesized 3-arylazo-4-hydroxybenzo[h]quinolin-2(1H)-one dyes. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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2
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Miniyar P, Mahajan A, Anuse D, Kumar A, Barmade M, Sarkar D, Arkile M, Khedkar V. Recursive Partitioning Analysis and Anti-Tubercular Screening of 3- Aminopyrazine-2-Carbohydrazide Derivatives. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180816666190329222636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Treating tuberculosis is a challenge due to the development of drug
resistance. Hence, it is imperative to develop novel leads having high potency and efficacy to curb
drug resistance.
Methods:
The present research work is focused on microwave-assisted synthesis of novel twenty-six
3-amino-N’-benzylidenepyrazine-2-carbohydrazide derivatives (3a-z), where, lyophilization
technique was used for isolation of the major intermediate, 3-aminopyrazin-2-carbohydrazide. All
synthesized compounds were subjected for anti-tubercular screening against Mycobacterium
tuberculosis H37Ra by using XTT Reduction Menadione Assay (XRMA) protocol.
Results:
Out of 26 synthesized compounds, four N’-substitutedbenzaldehyde-3-amino-pyrazine-2-
carbohydrazide derivatives viz. 3i, 3j 3v and 3z showed significant activity against M. tuberculosis
H37Ra. The compounds 3i, 3j, 3v and 3z showed 99, 98, 92 and 87 % inhibition respectively as
compared to 94% inhibition shown by the standard drug rifampicin. The MIC and IC50 values were in
the range of 24.3-110 and 5.9-20.8 µg/ml respectively.
Conclusion:
A classification model called Recursive Partitioning (RP) based on binary Quantitative
Structure-Activity Relationship (QSAR) was derived for the establishment of structure-activity
relationship (SAR). The predictions derived on the basis of RP model were found to be in agreement
with anti-tubercular screening data.
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Affiliation(s)
- Pankaj Miniyar
- Department of Pharmaceutical Chemistry, Sinhgad Institute of Pharmacy, Narhe, Pune- 411041, Affiliated to Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India
| | - Anand Mahajan
- Goa College of Pharmacy, 18th June Road, Panaji, Goa 403 001, India
| | - Dattatray Anuse
- Department of Pharmaceutical Chemistry, Sinhgad Institute of Pharmacy, Narhe, Pune- 411041, Affiliated to Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India
| | - Ashish Kumar
- Department of Pharmaceutical Chemistry, Sinhgad Institute of Pharmacy, Narhe, Pune- 411041, Affiliated to Savitribai Phule Pune University, Ganeshkhind, Pune 411007, India
| | | | - Dhiman Sarkar
- CombiChem Bio Resource Center, National Chemical Laboratory, Pune 411008, India
| | - Manisha Arkile
- CombiChem Bio Resource Center, National Chemical Laboratory, Pune 411008, India
| | - Vijay Khedkar
- CombiChem Bio Resource Center, National Chemical Laboratory, Pune 411008, India
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3
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Golbraikh A. Value of p-Value. Mol Inform 2019; 38:e1800152. [PMID: 31188542 DOI: 10.1002/minf.201800152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/07/2019] [Indexed: 11/09/2022]
Abstract
The goal of this manuscript is to discuss important aspects of external validation of classification and category Quantitative Structure - Activity/Property/Toxicity Relationship QS/A/P/T/R models that to the best of author's knowledge are not addressed in publications. Statistical significance (in terms of p-value) and accuracy of prediction (in terms of Correct Classification Rate (CCR)) of external validation set compounds are among most important characteristics of the models. We assert that in most cases the models built for classification or category response variable should be statistically significant and predictive for each class or category. We show that three thresholds of the number of compounds in each class or category of the external validation sets should be satisfied. 1) The p-value criterion can never be satisfied, if the number of compounds is below the first threshold. 2) If the number of compounds is between the first and the second thresholds, p-value criterion should be used. 3) If it is higher than the third threshold, classification or category accuracy criterion should be used. 4) If the number of compounds is between second and third thresholds, either one or the other criterion should be used depending on the value of p-value. 5) When the number of compounds in the class approaches infinity, the maximum relative error of prediction approaches the relative expected error. The results are of interest in other areas of multidimensional data analysis.
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Affiliation(s)
- Alexander Golbraikh
- Laboratory for Molecular Modeling, University of North Carolina at Chapel Hill, CB #7360, Chapel Hill, NC 27599
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4
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Deshmukh AR, Dhumal ST, Nawale LU, Khedkar VM, Sarkar D, Mane RA. Dicationic liquid mediated synthesis of tetrazoloquinolinyl methoxy phenyl 4-thiazolidinones and their antibacterial and antitubercular evaluation. SYNTHETIC COMMUN 2019. [DOI: 10.1080/00397911.2018.1564928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Amarsinh R. Deshmukh
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University , Aurangabad , India
| | - Sambhaji T. Dhumal
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University , Aurangabad , India
| | - Laxman U. Nawale
- CSIR-National Chemical Laboratory, Combi-Chem Bio Resource Centre , Pune , India
| | - Vijay M. Khedkar
- CSIR-National Chemical Laboratory, Combi-Chem Bio Resource Centre , Pune , India
| | - Dhiman Sarkar
- CSIR-National Chemical Laboratory, Combi-Chem Bio Resource Centre , Pune , India
| | - Ramrao A. Mane
- Department of Chemistry, Dr. Babasaheb Ambedkar Marathwada University , Aurangabad , India
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5
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Desai NC, Trivedi A, Somani H, Jadeja KA, Vaja D, Nawale L, Khedkar VM, Sarkar D. Synthesis, biological evaluation, and molecular docking study of pyridine clubbed 1,3,4-oxadiazoles as potential antituberculars. SYNTHETIC COMMUN 2018. [DOI: 10.1080/00397911.2017.1410892] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- N. C. Desai
- Division of Medicinal Chemistry, Department of Chemistry (DST-FIST Sponsored), Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, India
| | - Amit Trivedi
- Division of Medicinal Chemistry, Department of Chemistry (DST-FIST Sponsored), Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, India
| | - Hardik Somani
- Division of Medicinal Chemistry, Department of Chemistry (DST-FIST Sponsored), Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, India
| | - Krunalsinh A. Jadeja
- Division of Medicinal Chemistry, Department of Chemistry (DST-FIST Sponsored), Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, India
| | - Darshita Vaja
- Division of Medicinal Chemistry, Department of Chemistry (DST-FIST Sponsored), Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, India
| | - Laxman Nawale
- CSIR-National Chemical Laboratory, Combi Chem-Bio Resource Centre, Pune, India
| | - Vijay M. Khedkar
- Department of Pharmaceutical Chemistry, Shri Vile Parle Kelavani Mandal’s Institute of Pharmacy, Mumbai, India
| | - Dhiman Sarkar
- CSIR-National Chemical Laboratory, Combi Chem-Bio Resource Centre, Pune, India
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6
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7
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Al-zagameem AS, El-Abadelah MM, Zihlif MA, Naffa RG, Al-Smadi ML, Mubarak MS. Synthesis and Bioassay of Novel Substituted Pyrano[2,3- f]cinnoline-2-ones. J Heterocycl Chem 2016. [DOI: 10.1002/jhet.2482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | | | - Malek A. Zihlif
- Department of Pharmacology, Faculty of Medicine; The University of Jordan; Amman 11942 Jordan
| | - Randa G. Naffa
- Laboratory of Molecular Biology Research, Faculty of Medicine; The University of Jordan; Amman 11942 Jordan
| | - Musa L. Al-Smadi
- Chemistry Department, Faculty of Science and Arts; Jordan University of Science and Technology; Irbid 22110 Jordan
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8
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Desai NC, Kotadiya GM, Trivedi AR, Khedkar VM, Jha PC. Design, synthesis, and biological evaluation of novel fluorinated pyrazole encompassing pyridyl 1,3,4-oxadiazole motifs. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1683-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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9
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Synthesis, biological valuation, and QSAR studies of novel pyrazole bearing pyridyl oxadiazole analogues as potential antimicrobial agents. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1511-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Desai NC, Somani H, Trivedi A, Bhatt K, Nawale L, Khedkar VM, Jha PC, Sarkar D. Synthesis, biological evaluation and molecular docking study of some novel indole and pyridine based 1,3,4-oxadiazole derivatives as potential antitubercular agents. Bioorg Med Chem Lett 2016; 26:1776-83. [PMID: 26920799 DOI: 10.1016/j.bmcl.2016.02.043] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 02/10/2016] [Accepted: 02/16/2016] [Indexed: 11/16/2022]
Abstract
A series of indole and pyridine based 1,3,4-oxadiazole derivatives 5a-t were synthesized and evaluated for their in vitro antitubercular activity against Mycobacterium tuberculosis H37Ra (MTB) and Mycobacterium bovis BCG both in active and dormant state. Compounds 5b, 5e, 5g and 5q exhibited very good antitubercular activity. All the newly synthesized compounds 5a-t were further evaluated for anti-proliferative activity against HeLa, A549 and PANC-1 cell lines using modified MTT assay and found to be noncytotoxic. On the basis of cytotoxicity and MIC values against Mycobacterium bovis BCG, selectivity index (SI) of most active compounds 5b, 5e, 5g and 5q was calculated (SI=GI50/MIC) in active and dormant state. Compounds 5b, 5e and 5g demonstrated SI values ⩾10 against all three cell lines and were found to safe for advance screening. Compounds 5a-t were further screened for their antibacterial activity against four bacteria strains to assess their selectivity towards MTB. In addition, the molecular docking studies revealed the binding modes of these compounds in active site of enoyl reductase (InhA), which in turn helped to establish a structural basis of inhibition of mycobacteria. The potency, low cytotoxicity and selectivity of these compounds make them valid lead compounds for further optimization.
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Affiliation(s)
- N C Desai
- Division of Medicinal Chemistry, Department of Chemistry (DST-FIST Sponsored), Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar 364 002, Gujarat, India.
| | - Hardik Somani
- Division of Medicinal Chemistry, Department of Chemistry (DST-FIST Sponsored), Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar 364 002, Gujarat, India
| | - Amit Trivedi
- Division of Medicinal Chemistry, Department of Chemistry (DST-FIST Sponsored), Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar 364 002, Gujarat, India
| | - Kandarp Bhatt
- Division of Medicinal Chemistry, Department of Chemistry (DST-FIST Sponsored), Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar 364 002, Gujarat, India
| | - Laxman Nawale
- Combi Chem Bio Resource Centre, National Chemical Laboratory, Pune 411 008, India
| | - Vijay M Khedkar
- Combi Chem Bio Resource Centre, National Chemical Laboratory, Pune 411 008, India
| | - Prakash C Jha
- School of Chemical Sciences, Central University of Gujarat, Sector-30, Gandhinagar 382 030, Gujarat, India
| | - Dhiman Sarkar
- Combi Chem Bio Resource Centre, National Chemical Laboratory, Pune 411 008, India
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11
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Desai NC, Trivedi AR, Vaghani HV, Somani HC, Bhatt KA. Synthesis and biological evaluation of 1,3,4-oxadiazole bearing dihydropyrimidines as potential antitubercular agents. Med Chem Res 2015. [DOI: 10.1007/s00044-015-1485-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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12
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Stavrakov G, Valcheva V, Voynikov Y, Philipova I, Atanasova M, Konstantinov S, Peikov P, Doytchinova I. Design, Synthesis, and Antimycobacterial Activity of Novel Theophylline-7-Acetic Acid Derivatives With Amino Acid Moieties. Chem Biol Drug Des 2015; 87:335-41. [PMID: 26502828 DOI: 10.1111/cbdd.12676] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 09/13/2015] [Accepted: 10/12/2015] [Indexed: 01/18/2023]
Abstract
The theophylline-7-acetic acid (7-TAA) scaffold is a promising novel lead compound for antimycobacterial activity. Here, we derive a model for antitubercular activity prediction based on 14 7-TAA derivatives with amino acid moieties and their methyl esters. The model is applied to a combinatorial library, consisting of 40 amino acid and methyl ester derivatives of 7-TAA. The best three predicted compounds are synthesized and tested against Mycobacterium tuberculosis H37Rv. All of them are stable, non-toxic against human cells and show antimycobacterial activity in the nanomolar range being 60 times more active than ethambutol.
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Affiliation(s)
- Georgi Stavrakov
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav St., Sofia, 1000, Bulgaria
| | - Violeta Valcheva
- Institute of Microbiology, Bulgarian Academy of Sciences, 26 Akad. Bonchev St., Sofia, 1113, Bulgaria
| | - Yulian Voynikov
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav St., Sofia, 1000, Bulgaria
| | - Irena Philipova
- Institute of Organic Chemistry, Bulgarian Academy of Sciences, 9 Acad. Bonchev St., Sofia, 1113, Bulgaria
| | - Mariyana Atanasova
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav St., Sofia, 1000, Bulgaria
| | - Spiro Konstantinov
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav St., Sofia, 1000, Bulgaria
| | - Plamen Peikov
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav St., Sofia, 1000, Bulgaria
| | - Irini Doytchinova
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav St., Sofia, 1000, Bulgaria
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13
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Prediction on the inhibition ratio of pyrrolidine derivatives on matrix metalloproteinase based on gene expression programming. BIOMED RESEARCH INTERNATIONAL 2014; 2014:210672. [PMID: 24971318 PMCID: PMC4054925 DOI: 10.1155/2014/210672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/29/2014] [Indexed: 11/17/2022]
Abstract
Quantitative structure-activity relationships (QSAR) were developed to predict the inhibition ratio of pyrrolidine derivatives on matrix metalloproteinase via heuristic method (HM) and gene expression programming (GEP). The descriptors of 33 pyrrolidine derivatives were calculated by the software CODESSA, which can calculate quantum chemical, topological, geometrical, constitutional, and electrostatic descriptors. HM was also used for the preselection of 5 appropriate molecular descriptors. Linear and nonlinear QSAR models were developed based on the HM and GEP separately and two prediction models lead to a good correlation coefficient (R2) of 0.93 and 0.94. The two QSAR models are useful in predicting the inhibition ratio of pyrrolidine derivatives on matrix metalloproteinase during the discovery of new anticancer drugs and providing theory information for studying the new drugs.
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14
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Stavrakov G, Valcheva V, Philipova I, Doytchinova I. Design of novel camphane-based derivatives with antimycobacterial activity. J Mol Graph Model 2014; 51:7-12. [PMID: 24859319 DOI: 10.1016/j.jmgm.2014.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 04/02/2014] [Accepted: 04/21/2014] [Indexed: 01/19/2023]
Abstract
Although tuberculosis (TB) continues to be one of the leading infectious disease killers globally, it is curable and preventable. Despite the existence of safe, well tolerated and effective drugs used in the TB treatment, the interest in new entities, combinations and regimens increases during the last 10 years. Recently, we reported for a new class of anti-TB agents - camphane-based derivatives with nanomolar activity against Mycobacterium tuberculosis strains. The quantitative structure-activity relationship (QSAR) study on 12 compounds revealed several structural requirements for antimycobacterial activity: two hydrogen bond donors, two or three rings and no large branched substituents. Here, we describe the design of a set of nine novel camphane-based derivatives following these requirements. The compounds were synthesized and tested against M. tuberculosis strain H37Rv. Four of them showed activities in the nanomolar range, significantly higher than the activities in the initial set. The QSAR study based on all 21 derivatives pointed to two main structural requirements for anti-TB activity: two hydrogen bond donors and a side chain with aromatic ring.
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Affiliation(s)
- Georgi Stavrakov
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav st., Sofia 1000, Bulgaria
| | - Violeta Valcheva
- Institute of Microbiology, Bulgarian Academy of Sciences, 26 Akad. Bonchev st., Sofia 1113, Bulgaria
| | - Irena Philipova
- Institute of Organic Chemistry, Bulgarian Academy of Sciences, 9 Acad. Bonchev st., Sofia 1113, Bulgaria
| | - Irini Doytchinova
- Faculty of Pharmacy, Medical University of Sofia, 2 Dunav st., Sofia 1000, Bulgaria.
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