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Dhamodharan P, Pillai GG, Arumugam M. Identification of potential phytochemical inhibitors for the proven six chronic obstructive pulmonary disease biomarkers - A molecular dynamics study. J Biomol Struct Dyn 2023:1-26. [PMID: 37811632 DOI: 10.1080/07391102.2023.2259490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 09/08/2023] [Indexed: 10/10/2023]
Abstract
COPD is a multifactorial lung disease causing breathing difficulties in individuals and is becoming a major health concern worldwide. The unclear pathogenic mechanism and high mortality rate urge the development of drugs against this disease. In this study, around six COPD biomarkers identified from the preceding research through integrated gene expression analysis were taken as COPD target proteins. A total of 3307 phytocompounds were included in the COPD phytocompound library from 59 therapeutic plant sources. Furthermore, a crucial three-step virtual screening process (Absorption, Distribution, Metabolism, and Excretion, respiratory nontoxicity, less harmful and nontoxic compound category) was implemented to filter the potential drug-like phytocompounds. As a result, 160 phytocompounds were filtered with desired Absorption, Distribution, Metabolism, Excretion and Toxicity properties. The filtered 160 phytocompounds were docked against six COPD target proteins and the best-docked complexes were identified through visual inspection based on six unique parameters in SeeSAR. Furthermore, the best docked complexes were subjected to molecular dynamics simulation studies to assess the stability and conformational changes of the complexes. The presence of few amino acid residues within the crucial active, allosteric and catalytic sites of the six target proteins were revealed from the binding interaction types and major residual fluctuations from molecular docking and dynamic simulation studies respectively. This is indicative of the potential inhibitory activity of phytocompounds against the COPD biomarkers. Here we report the identified phytocompounds as a promising lead molecule for the six COPD biomarkers through in silico analysis opening new avenues in COPD pathogenesis and treatments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pavithra Dhamodharan
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | | | - Mohanapriya Arumugam
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Panda SS, Tran QL, Rajpurohit P, Pillai GG, Thomas SJ, Bridges AE, Capito JE, Thangaraju M, Lokeshwar BL. Design, Synthesis, and Molecular Docking Studies of Curcumin Hybrid Conjugates as Potential Therapeutics for Breast Cancer. Pharmaceuticals (Basel) 2022; 15:ph15040451. [PMID: 35455448 PMCID: PMC9028889 DOI: 10.3390/ph15040451] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/06/2023] Open
Abstract
Curcumin (CUR) has received great attention over the past two decades due to its anticancer, anti-inflammatory, and antioxidant properties. Similarly, Dichloroacetate (DCA), an pyruvate dehydrogenase kinase 1 (PKD1) inhibitor, has gained huge attention as a potential anticancer drug. However, the clinical utility of these two agents is very limited because of the poor bioavailability and unsolicited side effects, respectively. We have synthesized fusion conjugates of CUR and DCA with an amino acids linker to overcome these limitations by utilizing the molecular hybridization approach. The molecular docking studies showed the potential targets of Curcumin-Modified Conjugates (CMCs) in breast cancer cells. We synthesized six hybrid conjugates named CMC1-6. These six CMC conjugates do not show any significant toxicity in a human normal immortalized mammary epithelial cell line (MCF10A) in vitro and C57BL/6 mice in vivo. However, treatment with CMC1 and CMC2 significantly reduced the growth and clonogenic survival by colony-formation assays in several human breast cancer cells (BC). Treatment by oral gavage of a transgenic mouse BC and metastatic BC tumor-bearing mice with CMC2 significantly reduced tumor growth and metastasis. Overall, our study provides strong evidence that CUR and DCA conjugates have a significant anticancer properties at a sub-micromolar concentration and overcome the clinical limitation of using CUR and DCA as potential anticancer drugs.
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Affiliation(s)
- Siva S. Panda
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30912, USA; (Q.L.T.); (S.J.T.); (J.E.C.)
- Correspondence: (S.S.P.); (M.T.)
| | - Queen L. Tran
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30912, USA; (Q.L.T.); (S.J.T.); (J.E.C.)
| | - Pragya Rajpurohit
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, USA; (P.R.); (A.E.B.); (B.L.L.)
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
| | | | - Sean J. Thomas
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30912, USA; (Q.L.T.); (S.J.T.); (J.E.C.)
| | - Allison E. Bridges
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, USA; (P.R.); (A.E.B.); (B.L.L.)
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
| | - Jason E. Capito
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30912, USA; (Q.L.T.); (S.J.T.); (J.E.C.)
| | - Muthusamy Thangaraju
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, USA; (P.R.); (A.E.B.); (B.L.L.)
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
- Correspondence: (S.S.P.); (M.T.)
| | - Bal L. Lokeshwar
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, USA; (P.R.); (A.E.B.); (B.L.L.)
- Georgia Cancer Center, Augusta University, Augusta, GA 30912, USA
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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Ambili Unni P, Pillai GG, Sajitha Lulu S. Developing a molecular roadmap to Narasimha Rasayana: A system Polypharmacology approach. Gene Reports 2022. [DOI: 10.1016/j.genrep.2021.101488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Prakash V, Krishnan AS, Ramesh R, Bose C, Pillai GG, Nair BG, Pal S. Synergistic Effects of Limosilactobacillus fermentum ASBT-2 with Oxyresveratrol Isolated from Coconut Shell Waste. Foods 2021; 10:foods10112548. [PMID: 34828830 PMCID: PMC8622123 DOI: 10.3390/foods10112548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
Value-added phytochemicals from food by-products and waste materials have gained much interest and among them, dietary polyphenolic compounds with potential biological properties extend a promising sustainable approach. Oxyresveratrol (Oxy), a stilbenoid polyphenol, possesses great therapeutic potential, though its pharmacokinetic issues need attention. A good source of oxyresveratrol was found in underutilized coconut shells and the synbiotic applications of the compound in combination with a potential probiotic isolate Limosilactobacillus fermentum ASBT-2 was investigated. The compound showed lower inhibitory effects on the strain with minimum inhibitory concentration (MIC) of 1000 µg/mL. Oxyresveratrol at sub-MIC concentrations (500 µg/mL and 250 µg/mL) enhanced the probiotic properties without exerting any inhibitory effects on the strain. The combination at sub- MIC concentration of the compound inhibited Salmonella enterica and in silico approaches were employed to elucidate the possible mode of action of oxy on the pathogen. Thus, the combination could target pathogens in the gut without exerting negative impacts on growth of beneficial strains. This approach could be a novel perspective to address the poor pharmacokinetic properties of the compound.
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Affiliation(s)
- Vidhya Prakash
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India; (V.P.); (A.S.K.); (R.R.); (C.B.); (B.G.N.)
| | - Akshaya S Krishnan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India; (V.P.); (A.S.K.); (R.R.); (C.B.); (B.G.N.)
| | - Reshma Ramesh
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India; (V.P.); (A.S.K.); (R.R.); (C.B.); (B.G.N.)
| | - Chinchu Bose
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India; (V.P.); (A.S.K.); (R.R.); (C.B.); (B.G.N.)
| | | | - Bipin G. Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India; (V.P.); (A.S.K.); (R.R.); (C.B.); (B.G.N.)
| | - Sanjay Pal
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India; (V.P.); (A.S.K.); (R.R.); (C.B.); (B.G.N.)
- Correspondence: ; Tel.: +91-4762805315
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Bokhtia RM, Panda SS, Girgis AS, Pillai GG, Ibrahim TS, Shalaby EM, Gigli L, Abdel‐Aal EH, Al‐Mahmoudy AMM. Efficient Synthesis and Computational Studies of Useful Guanylating Agents: 1
H
‐Benzotriazole‐1‐carboximidamides. ChemistrySelect 2020. [DOI: 10.1002/slct.202003796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Riham M. Bokhtia
- Department of Chemistry & Physics Augusta University 1120 15th Street Augusta GA 30912 USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy Zagazig University Zagazig, 44519 Egypt
| | - Siva S. Panda
- Department of Chemistry & Physics Augusta University 1120 15th Street Augusta GA 30912 USA
| | - Adel S. Girgis
- Department of Pesticide Chemistry National Research Centre Dokki Giza 12622 Egypt
| | | | - Tarek S. Ibrahim
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy Zagazig University Zagazig, 44519 Egypt
- Department of Pharmaceutical Chemistry King Abdulaziz University Jeddah 21589 Saudi Arabia
| | - ElSayed M. Shalaby
- X-Ray Crystallography Lab. Physics Division National Research Centre Dokki Giza 12622 Egypt
| | - Lara Gigli
- Elettra-Sincrotrone Trieste s.s. 14 Km 163.5 in Area Science Park, Basovizza Trieste 34149 Italy
| | - Eatedal H. Abdel‐Aal
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy Zagazig University Zagazig, 44519 Egypt
| | - Amany M. M. Al‐Mahmoudy
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy Zagazig University Zagazig, 44519 Egypt
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Affiliation(s)
- Kiran Bajaj
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India
| | | | - Rajeev Sakhuja
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India
| | - Dalip Kumar
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India
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Unni P A, Sudhakaran SL, Pillai GG. Review on druggable targets of key age-associated properties regulated by therapeutic agents. Chem Biol Drug Des 2020; 96:1069-1083. [PMID: 32679616 DOI: 10.1111/cbdd.13759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/27/2020] [Accepted: 07/05/2020] [Indexed: 11/28/2022]
Abstract
Aging is a biological process which accounts for the deterioration of effective physiological functions. The malfunctioning of vital organ systems leads to the onset of neurodegenerative, cardiovascular, and immunomodulatory diseases in the elder population. Age-dependent mitochondrial dysfunctions trigger the production of reactive oxygen species, which serve as a major contributing factor for the onset of age-associated diseases. The increasing burden of age-related pathologies explicates the relevance of identifying novel therapeutic agents with enhanced potency and bioavailability. Key information on the biological mechanisms of significant age-related diseases aids in understanding relevant druggable targets essential for the initiation and progression of the disease. This review provides detailed insights into the druggable targets of key anti-aging properties of therapeutic agents such as anti-oxidant, immunomodulation, cardioprotection, anti-melanogenic, and anti-elastase properties. This information aids in the development of novel therapeutic agents/ supplements with enhanced efficacy.
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Affiliation(s)
- Ambili Unni P
- School of Biosciences and Technology, VIT, Vellore, India
| | | | - Girinath G Pillai
- School of Biosciences and Technology, VIT, Vellore, India.,Nyro Research India, Kochi, Kerala, India
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Unni PA, Lulu SS, Pillai GG. Computational strategies towards developing novel antimelanogenic agents. Life Sci 2020; 250:117602. [PMID: 32240677 DOI: 10.1016/j.lfs.2020.117602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 03/12/2020] [Accepted: 03/22/2020] [Indexed: 11/30/2022]
Abstract
AIMS Extrinsic ageing or photoageing relates to the onset of age-linked phenotypes such as skin hyperpigmentation due to UV exposure. UV induced upregulated production of tyrosinase enzyme, which catalyses the vital biochemical reactions of melanin synthesis is responsible for the inception of skin hyperpigmentation. We aimed to generate a validated QSAR model with a dataset consisting of 69 thio-semicarbazone derivatives to elucidate the physicochemical properties of compounds essential for tyrosinase inhibition and to identify novel lead molecules with enhanced tyrosinase inhibitory activity and bioavailability. MAIN METHODS Lead optimization and insilico approaches were employed in this research work. QSAR model was generated and validated by exploiting Multiple Linear Regression method. Prioritization of lead-like compounds was accomplished by performing multi parameter optimization depleting molecular docking, bioavailability assessments and toxicity prediction for 69 compounds Derivatives of best lead compound were retrieved from chemical spaces. KEY FINDINGS Molecular descriptors explicated the significance of chemical properties essential for chelation of copper ions present in the active site of tyrosinase protein target. Further, derivatives which comprise of electron donating groups in their chemical structure were predicted and analysed for tyrosinase inhibitory activity by employing insilico methodologies including chemical space exploration. SIGNIFICANCE Our research work resulted in the generation of a validated QSAR model with higher degree of external predictive ability and significance to tyrosinase inhibitory activity. We propose 11 novel derivative compounds with enhanced tyrosinase inhibitory activity and bioavailability.
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Affiliation(s)
- P Ambili Unni
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - S Sajitha Lulu
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Girinath G Pillai
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India; Nyro Research India, Kochi, Kerala, India.
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9
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Mary YS, Mary YS, Thomas R, Narayana B, Samshuddin S, Sarojini BK, Armaković S, Armaković SJ, Pillai GG. Theoretical Studies on the Structure and Various Physico-Chemical and Biological Properties of a Terphenyl Derivative with Immense Anti-Protozoan Activity. Polycycl Aromat Compd 2019. [DOI: 10.1080/10406638.2019.1624974] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Y. Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Y. Shyma Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - B. Narayana
- Department of Chemistry, Mangalore University, Mangalagangothri, Karnataka, India
| | - S. Samshuddin
- Department of Chemistry, Mangalore University, Mangalagangothri, Karnataka, India
- Department of Chemistry, SDM Institute of Technology, Ujire, Karnataka, India
| | - B. K. Sarojini
- Department of Industrial Chemistry, Mangalore University, Mangalagangothri, Karnataka, India
| | - Stevan Armaković
- Department of Physics, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Sanja J. Armaković
- Department of Chemistry, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
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Abstract
A one-pot ligation strategy at aspartic acid junction has been described by incorporating aziridin-2,3-dicarboxylate to the N-side of a peptide fragment that ligates with a variety of small peptide thio acids to afford native peptides in good yields.
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Affiliation(s)
- Kiran Bajaj
- Department of Chemistry
- Birla Institute of Technology and Science
- Pilani 333031
- India
| | - Devesh S. Agarwal
- Department of Chemistry
- Birla Institute of Technology and Science
- Pilani 333031
- India
| | - Rajeev Sakhuja
- Department of Chemistry
- Birla Institute of Technology and Science
- Pilani 333031
- India
| | - Girinath G. Pillai
- Computational Chemistry Division
- Zastra Innovations Pvt. Ltd
- Bengaluru 560043
- India
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Chowdhury L, Croft CJ, Goel S, Zaman N, Tai ACS, Walch EM, Smith K, Page A, Shea KM, Hall CD, Jishkariani D, Pillai GG, Hall AC. Differential Potency of 2,6-Dimethylcyclohexanol Isomers for Positive Modulation of GABAA Receptor Currents. J Pharmacol Exp Ther 2016; 357:570-9. [PMID: 27029583 DOI: 10.1124/jpet.115.228890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 03/22/2016] [Indexed: 11/22/2022] Open
Abstract
GABAA receptors meet all of the pharmacological requirements necessary to be considered important targets for the action of general anesthetic agents in the mammalian brain. In the following patch-clamp study, the relative modulatory effects of 2,6-dimethylcyclohexanol diastereomers were investigated on human GABAA (α1β3γ2s) receptor currents stably expressed in human embryonic kidney cells. Cis,cis-, trans,trans-, and cis,trans-isomers were isolated from commercially available 2,6-dimethylcyclohexanol and were tested for positive modulation of submaximal GABA responses. For example, the addition of 30 μM cis,cis-isomer resulted in an approximately 2- to 3-fold enhancement of the EC20 GABA current. Coapplications of 30 μM 2,6-dimethylcyclohexanol isomers produced a range of positive enhancements of control GABA responses with a rank order for positive modulation: cis,cis > trans,trans ≥ mixture of isomers > > cis,trans-isomer. In molecular modeling studies, the three cyclohexanol isomers bound with the highest binding energies to a pocket within transmembrane helices M1 and M2 of the β3 subunit through hydrogen-bonding interactions with a glutamine at the 224 position and a tyrosine at the 220 position. The energies for binding to and hydrogen-bond lengths within this pocket corresponded with the relative potencies of the agents for positive modulation of GABAA receptor currents (cis,cis > trans,trans > cis,trans-2,6-dimethylcyclohexanol). In conclusion, the stereochemical configuration within the dimethylcyclohexanols is an important molecular feature in conferring positive modulation of GABAA receptor activity and for binding to the receptor, a consideration that needs to be taken into account when designing novel anesthetics with enhanced therapeutic indices.
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Affiliation(s)
- Luvana Chowdhury
- Neuroscience Program, Departments of Biological Sciences (L.C., C.J.C., S.G., N.Z., A.C.-S.T., E.M.W., A.C.H.) and Chemistry (K.S., A.P., K.M.S.), Smith College, Northampton, Massachusetts; Department of Chemistry, University of Florida, Gainesville, Florida (C.D.H., D.J., G.G.P.); and Department of Chemistry, University of Tartu, Ravila, Estonia (G.G.P.)
| | - Celine J Croft
- Neuroscience Program, Departments of Biological Sciences (L.C., C.J.C., S.G., N.Z., A.C.-S.T., E.M.W., A.C.H.) and Chemistry (K.S., A.P., K.M.S.), Smith College, Northampton, Massachusetts; Department of Chemistry, University of Florida, Gainesville, Florida (C.D.H., D.J., G.G.P.); and Department of Chemistry, University of Tartu, Ravila, Estonia (G.G.P.)
| | - Shikha Goel
- Neuroscience Program, Departments of Biological Sciences (L.C., C.J.C., S.G., N.Z., A.C.-S.T., E.M.W., A.C.H.) and Chemistry (K.S., A.P., K.M.S.), Smith College, Northampton, Massachusetts; Department of Chemistry, University of Florida, Gainesville, Florida (C.D.H., D.J., G.G.P.); and Department of Chemistry, University of Tartu, Ravila, Estonia (G.G.P.)
| | - Naina Zaman
- Neuroscience Program, Departments of Biological Sciences (L.C., C.J.C., S.G., N.Z., A.C.-S.T., E.M.W., A.C.H.) and Chemistry (K.S., A.P., K.M.S.), Smith College, Northampton, Massachusetts; Department of Chemistry, University of Florida, Gainesville, Florida (C.D.H., D.J., G.G.P.); and Department of Chemistry, University of Tartu, Ravila, Estonia (G.G.P.)
| | - Angela C-S Tai
- Neuroscience Program, Departments of Biological Sciences (L.C., C.J.C., S.G., N.Z., A.C.-S.T., E.M.W., A.C.H.) and Chemistry (K.S., A.P., K.M.S.), Smith College, Northampton, Massachusetts; Department of Chemistry, University of Florida, Gainesville, Florida (C.D.H., D.J., G.G.P.); and Department of Chemistry, University of Tartu, Ravila, Estonia (G.G.P.)
| | - Erin M Walch
- Neuroscience Program, Departments of Biological Sciences (L.C., C.J.C., S.G., N.Z., A.C.-S.T., E.M.W., A.C.H.) and Chemistry (K.S., A.P., K.M.S.), Smith College, Northampton, Massachusetts; Department of Chemistry, University of Florida, Gainesville, Florida (C.D.H., D.J., G.G.P.); and Department of Chemistry, University of Tartu, Ravila, Estonia (G.G.P.)
| | - Kelly Smith
- Neuroscience Program, Departments of Biological Sciences (L.C., C.J.C., S.G., N.Z., A.C.-S.T., E.M.W., A.C.H.) and Chemistry (K.S., A.P., K.M.S.), Smith College, Northampton, Massachusetts; Department of Chemistry, University of Florida, Gainesville, Florida (C.D.H., D.J., G.G.P.); and Department of Chemistry, University of Tartu, Ravila, Estonia (G.G.P.)
| | - Alexandra Page
- Neuroscience Program, Departments of Biological Sciences (L.C., C.J.C., S.G., N.Z., A.C.-S.T., E.M.W., A.C.H.) and Chemistry (K.S., A.P., K.M.S.), Smith College, Northampton, Massachusetts; Department of Chemistry, University of Florida, Gainesville, Florida (C.D.H., D.J., G.G.P.); and Department of Chemistry, University of Tartu, Ravila, Estonia (G.G.P.)
| | - Kevin M Shea
- Neuroscience Program, Departments of Biological Sciences (L.C., C.J.C., S.G., N.Z., A.C.-S.T., E.M.W., A.C.H.) and Chemistry (K.S., A.P., K.M.S.), Smith College, Northampton, Massachusetts; Department of Chemistry, University of Florida, Gainesville, Florida (C.D.H., D.J., G.G.P.); and Department of Chemistry, University of Tartu, Ravila, Estonia (G.G.P.)
| | - C Dennis Hall
- Neuroscience Program, Departments of Biological Sciences (L.C., C.J.C., S.G., N.Z., A.C.-S.T., E.M.W., A.C.H.) and Chemistry (K.S., A.P., K.M.S.), Smith College, Northampton, Massachusetts; Department of Chemistry, University of Florida, Gainesville, Florida (C.D.H., D.J., G.G.P.); and Department of Chemistry, University of Tartu, Ravila, Estonia (G.G.P.)
| | - D Jishkariani
- Neuroscience Program, Departments of Biological Sciences (L.C., C.J.C., S.G., N.Z., A.C.-S.T., E.M.W., A.C.H.) and Chemistry (K.S., A.P., K.M.S.), Smith College, Northampton, Massachusetts; Department of Chemistry, University of Florida, Gainesville, Florida (C.D.H., D.J., G.G.P.); and Department of Chemistry, University of Tartu, Ravila, Estonia (G.G.P.)
| | - Girinath G Pillai
- Neuroscience Program, Departments of Biological Sciences (L.C., C.J.C., S.G., N.Z., A.C.-S.T., E.M.W., A.C.H.) and Chemistry (K.S., A.P., K.M.S.), Smith College, Northampton, Massachusetts; Department of Chemistry, University of Florida, Gainesville, Florida (C.D.H., D.J., G.G.P.); and Department of Chemistry, University of Tartu, Ravila, Estonia (G.G.P.)
| | - Adam C Hall
- Neuroscience Program, Departments of Biological Sciences (L.C., C.J.C., S.G., N.Z., A.C.-S.T., E.M.W., A.C.H.) and Chemistry (K.S., A.P., K.M.S.), Smith College, Northampton, Massachusetts; Department of Chemistry, University of Florida, Gainesville, Florida (C.D.H., D.J., G.G.P.); and Department of Chemistry, University of Tartu, Ravila, Estonia (G.G.P.)
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Bajaj K, Sakhuja R, Pillai GG. Traceless reductive ligation at a tryptophan site: a facile access to β-hydroxytryptophan appended peptides. Org Biomol Chem 2016; 14:9578-9587. [DOI: 10.1039/c6ob01542e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One-pot methodology (reduction & O to N migration); synthesis of β-hydroxytryptophan appended native peptides; computational support for the mechanism.
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Affiliation(s)
- Kiran Bajaj
- Department of Chemistry
- Birla Institute of Technology and Science
- Pilani 333031
- India
| | - Rajeev Sakhuja
- Department of Chemistry
- Birla Institute of Technology and Science
- Pilani 333031
- India
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13
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Pillai GG, Sikk L, Tamm T, Karelson M, Burk P, Tämm K. Theoretical modeling of HPV: QSAR and novodesign with fragment approach. Curr Comput Aided Drug Des 2015; 10:303-14. [PMID: 25479379 DOI: 10.2174/1574886309666141126145756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 10/13/2014] [Accepted: 11/25/2014] [Indexed: 11/22/2022]
Abstract
Structure-activity relationships in a data set of HPV6-E1 helicase ATPase inhibitors were investigated based on two different sets of descriptors. Statistically significant four parameter Quantitative Structure-Activity Relationships (QSAR) models were constructed and validated in both cases (R(2)=0.849; R(2) cv=0.811; F=52.20; s(2)=0.25; N=42). A Fragment based QSAR (FQSAR) approach was applied for developing a fragment-QSAR equation, which enabled the construction of virtual structures for novel ATPase inhibitors with desired or pre-defined activity.
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Affiliation(s)
| | | | | | | | | | - Kaido Tämm
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia.
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14
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Pillai GG, Mederos L, Panda CS, Gronski A, Burk P, Hall CD, Katritzky AR, Tämm K, Karelson M. Robust Modeling and Scaffold Hopping: Case Study Based on HIV Reverse Transcriptase Inhibitors Type-1 Data. Med Chem 2015; 12:513-26. [PMID: 26434799 DOI: 10.2174/1573406411666151005110141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 10/02/2015] [Accepted: 10/02/2015] [Indexed: 11/22/2022]
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) is the causative agent of AIDS occurs across mucosal surfaces or by direct inoculation. OBJECTIVE The objective of this study was to consider chemically diverse scaffold sets of HIV-1 Reverse Transcriptase Inhibitors (HIV-1 RTI) subjected to ideal oriented QSAR with large descriptor space. METHOD We generated a four-parameter QSAR model based on 111 data points, which provided an optimum prediction of HIV-1 RTI for overall 367 experimentally measured compounds. RESULTS The robustness of the model is demonstrated by its statistical validation (Ntraining = 111, R2 = 0.85, Q2lmo = 0.84) and by the prediction of HIV-1 inhibition activity for experimentally measured compounds. CONCLUSION Finally, 5 novel hit compounds were designed in silico by using a virtual screening approach. The new hits met all the pharmacophore constraints and predicted pIC50 values within the binding ability of HIV-1 RT protein targets.
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Affiliation(s)
- Girinath G Pillai
- Department of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia.
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15
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Dearden JC, Hewitt M, Roberts DW, Enoch SJ, Rowe PH, Przybylak KR, Vaughan-Williams GD, Smith ML, Pillai GG, Katritzky AR. Mechanism-Based QSAR Modeling of Skin Sensitization. Chem Res Toxicol 2015; 28:1975-86. [PMID: 26382665 DOI: 10.1021/acs.chemrestox.5b00197] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many chemicals can induce skin sensitization, and there is a pressing need for non-animal methods to give a quantitative indication of potency. Using two large published data sets of skin sensitizers, we have allocated each sensitizing chemical to one of 10 mechanistic categories and then developed good QSAR models for the seven categories that have a sufficient number of chemicals to allow modeling. Both internal and external validation checks showed that each model had good predictivity.
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Affiliation(s)
- J C Dearden
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, United Kingdom
| | - M Hewitt
- School of Pharmacy, University of Wolverhampton , Wulfruna Street, Wolverhampton WV1 1LY, United Kingdom
| | - D W Roberts
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, United Kingdom
| | - S J Enoch
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, United Kingdom
| | - P H Rowe
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, United Kingdom
| | - K R Przybylak
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, United Kingdom
| | - G D Vaughan-Williams
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, United Kingdom
| | - M L Smith
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University , Byrom Street, Liverpool L3 3AF, United Kingdom
| | - G G Pillai
- Department of Chemistry, University of Florida , Gainsville, Florida 32611-7200, United States.,Institute of Chemistry, University of Tartu , 50411 Tartu, Estonia
| | - A R Katritzky
- Department of Chemistry, University of Florida , Gainsville, Florida 32611-7200, United States
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16
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Girgis AS, Panda SS, Farag ISA, El-Shabiny AM, Moustafa AM, Ismail NSM, Pillai GG, Panda CS, Hall CD, Katritzky AR. Synthesis, and QSAR analysis of anti-oncological active spiro-alkaloids. Org Biomol Chem 2015; 13:1741-53. [PMID: 25502495 DOI: 10.1039/c4ob02149e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
QSAR study describes the anti-neoplastic spiro-alkaloids with relevant molecular descriptors using CODESSA III software. The dispiro[3H-indole-3,2'-pyrrolidine-3',3"-piperidines] 24-48 were synthesized via [3 + 2]-cycloaddition reaction of azomethine ylides, (generated in situ via decarboxylative condensation of isatins 21-23 with sarcosine) and 3E,5E-1-alkyl-3,5-bis(arylmethylidene)-4-piperidones 10-20. Some of the synthesized analogues exhibited promising antitumor properties against HELA (cervical), HEPG2 (liver), T-47D, MCF7 (breast), and HCT116 (colon) human tumor cell lines, demonstrating activity close to or even better than the standard Doxorubicin, based on in vitro Sulfo-Rhodamine-B bio-assay.
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Affiliation(s)
- Adel S Girgis
- Pesticide Chemistry Department, National Research Centre, Dokki, Cairo 12622, Egypt
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17
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Ibrahim MA, Panda SS, Oliferenko AA, Oliferenko PV, Girgis AS, Elagawany M, Küçükbay FZ, Panda CS, Pillai GG, Samir A, Tämm K, Hall CD, Katritzky AR. Macrocyclic peptidomimetics with antimicrobial activity: synthesis, bioassay, and molecular modeling studies. Org Biomol Chem 2015; 13:9492-503. [PMID: 26256838 DOI: 10.1039/c5ob01400j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel, cyclic peptidomimetics were synthesized by facile acylation reactions using benzotriazole chemistry. Microbiological testing of the synthesized compounds revealed an exceptionally high activity against Candida albicans with a minimum inhibitory concentration (MIC) two orders of magnitude lower than the MIC of the antifungal reference drug amphotericin B. A strikingly high activity was also observed against three Gram-negative bacterial strains (Pseudomonas aeruginosa, Klebsiella pneumoniae and Proteus vulgaris), two of which are known human pathogens. Thus the discovered chemotype is a potential polypharmacological agent. The toxicity against mammalian tumor cells was found to be low, as demonstrated in five different human cell lines (HeLa, cervical; PC-3, prostate; MCF-7, breast; HepG2, liver; and HCT-116, colon). The internal consistency of the experimental data was studied using 3D-pharmacophore and 2D-QSAR.
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Affiliation(s)
- Mohamed A Ibrahim
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA.
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18
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Wang Z, Zhang H, Killian BJ, Jabeen F, Pillai GG, Berman HM, Mathelier M, Sibble AJ, Yeung J, Zhou W, Steel PJ, Hall CD, Katritzky AR. Synthesis, Characterization and Energetic Properties of 1,3,4-Oxadiazoles. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500583] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Girgis AS, Saleh DO, George RF, Srour AM, Pillai GG, Panda CS, Katritzky AR. Synthesis, bioassay, and QSAR study of bronchodilatory active 4H-pyrano[3,2-c]pyridine-3-carbonitriles. Eur J Med Chem 2015; 89:835-43. [DOI: 10.1016/j.ejmech.2013.12.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/27/2013] [Accepted: 12/21/2013] [Indexed: 10/25/2022]
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20
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Li Z, Lebedyeva I, Zhao D, Myers L, Pillai GG, Hall CD, Katritzky AR. Synthesis of L-Lys-Aminoxy-Goralatide. J Pept Sci 2014; 20:923-7. [PMID: 25331328 DOI: 10.1002/psc.2702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/15/2014] [Accepted: 08/27/2014] [Indexed: 11/09/2022]
Abstract
Natural tetrapeptide Goralatide inhibits primitive hematopoietic cell proliferation but reported to be rather unstable in solution (half-life 4.5 min). In this work, we report the synthesis of an aminoxy analog of Goralatide. Aminoxy moiety is expected to provide increased stability and bioavailability of the Goralatide analog.
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Affiliation(s)
- Zhiliang Li
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, PO Box: 117200, Gainesville, FL, 32611-7200, USA
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21
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Jabeen F, Oliferenko PV, Oliferenko AA, Pillai GG, Ansari FL, Hall CD, Katritzky AR. Dual inhibition of the α-glucosidase and butyrylcholinesterase studied by Molecular Field Topology Analysis. Eur J Med Chem 2014; 80:228-42. [DOI: 10.1016/j.ejmech.2014.04.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 04/03/2014] [Accepted: 04/04/2014] [Indexed: 01/22/2023]
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22
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Biswas S, Kayaleh R, Pillai GG, Seon C, Roberts I, Popov V, Alamry KA, Katritzky AR. Long-Range Chemical Ligation from N→N Acyl Migrations in Tryptophan Peptides via Cyclic Transition States of 10- to 18-Members. Chemistry 2014; 20:8189-98. [DOI: 10.1002/chem.201400125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Indexed: 11/07/2022]
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23
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Oliferenko PV, Oliferenko AA, Girgis AS, Saleh DO, Srour AM, George RF, Pillai GG, Panda CS, Hall CD, Katritzky AR. Synthesis, Bioassay, and Molecular Field Topology Analysis of Diverse Vasodilatory Heterocycles. J Chem Inf Model 2014; 54:1103-16. [DOI: 10.1021/ci400723m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Polina V. Oliferenko
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Alexander A. Oliferenko
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Adel S. Girgis
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | | | | | - Riham F. George
- Pharmaceutical
Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Girinath G. Pillai
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
- Department
of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
| | - Chandramukhi S. Panda
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - C. Dennis Hall
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Alan R. Katritzky
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
- Department
of Chemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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24
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Ha K, Lebedyeva I, Hamedzadeh S, Li Z, Quiñones R, Pillai GG, Williams B, Nasajpour A, Martin K, Asiri AM, Katritzky AR. Tandem Deprotection-Dimerization-Macrocyclization Route toC2Symmetriccyclo-Tetrapeptides. Chemistry 2014; 20:4874-9. [DOI: 10.1002/chem.201304262] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/24/2013] [Indexed: 11/08/2022]
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25
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Oliferenko PV, Oliferenko AA, Poda GI, Osolodkin DI, Pillai GG, Bernier UR, Tsikolia M, Agramonte NM, Clark GG, Linthicum KJ, Katritzky AR. Promising Aedes aegypti repellent chemotypes identified through integrated QSAR, virtual screening, synthesis, and bioassay. PLoS One 2013; 8:e64547. [PMID: 24039693 PMCID: PMC3765160 DOI: 10.1371/journal.pone.0064547] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 04/15/2013] [Indexed: 11/19/2022] Open
Abstract
Molecular field topology analysis, scaffold hopping, and molecular docking were used as complementary computational tools for the design of repellents for Aedes aegypti, the insect vector for yellow fever, chikungunya, and dengue fever. A large number of analogues were evaluated by virtual screening with Glide molecular docking software. This produced several dozen hits that were either synthesized or procured from commercial sources. Analysis of these compounds by a repellent bioassay resulted in a few highly active chemicals (in terms of minimum effective dosage) as viable candidates for further hit-to-lead and lead optimization effort.
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Affiliation(s)
- Polina V. Oliferenko
- Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
| | - Alexander A. Oliferenko
- Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
| | - Gennadiy I. Poda
- Medicinal Chemistry Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Girinath G. Pillai
- Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | | | | | | | | | | | - Alan R. Katritzky
- Department of Chemistry, University of Florida, Gainesville, Florida, United States of America
- Chemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
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26
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Ha K, Lebedyeva I, Li Z, Martin K, Williams B, Faby E, Nasajpour A, Pillai GG, Al-Youbi AO, Katritzky AR. Conformationally Assisted Lactamizations for the Synthesis of Symmetrical and Unsymmetrical Bis-2,5-diketopiperazines. J Org Chem 2013; 78:8510-23. [DOI: 10.1021/jo401235k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Khanh Ha
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Iryna Lebedyeva
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Zhiliang Li
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Kristin Martin
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Byron Williams
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Eric Faby
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Amir Nasajpour
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Girinath G. Pillai
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
- Institute of Chemistry, University of Tartu, Tartu 50411, Estonia
| | - Abdulrahman O. Al-Youbi
- Chemistry Department, Faculty
of Science, King Abdulaziz University,
Jeddah, 21589 Saudi Arabia
| | - Alan R. Katritzky
- Center for Heterocyclic
Compounds,
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
- Chemistry Department, Faculty
of Science, King Abdulaziz University,
Jeddah, 21589 Saudi Arabia
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27
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El-Gendy BEDM, Ghazvini Zadeh EH, Sotuyo AC, Pillai GG, Katritzky AR. α-Substitution Effects on the Ease ofS→N-Acyl Transfer in Aminothioesters. Chem Biol Drug Des 2013. [DOI: 10.1111/cbdd.12092] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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28
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Singh NK, Pakkkianathan BC, Kumar M, Daddam JR, Jayavel S, Kannan M, Pillai GG, Krishnan M. Computational studies on molecular interactions of 6-thioguanosine analogs with anthrax toxin receptor 1. Interdiscip Sci 2013; 4:183-9. [PMID: 23292691 DOI: 10.1007/s12539-012-0126-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 01/27/2012] [Accepted: 04/06/2012] [Indexed: 02/06/2023]
Abstract
Dormant endospores of Bacillus anthracis are the causative agent of anthrax, which is an acute disease for both human and animals. Anthrax has been practised as biological weapon because of two attributes: i) short duration of spore germination, and ii) lethal toxaemia of the vegetative stage. Pathogenesis is caused by the activity of edema toxin and lethal toxin. Protective antigen (PA), is an essential component of both complexes, binds to Anthrax Toxin Receptor (ATR) and mediates the lethality in mammals. The combination of vaccine and antibiotics are preferred to be effective treatment for destruction of the vegetative cell wall but could not be a successive destructor for endospores. So the present study is intended to identify the small molecules as a potential inhibitor for ATR1. 3D structure of Anthrax Toxin Receptor 1 (ATR1) was built by using the crystal structure of Anthrax Toxin Receptor 2 (ATR2) from Homo sapiens as template. Molecular docking of 6-thiogunaosine (6-TG) analogs was performed on the ATR1 model and effective inhibitor was selected based on the docking results. The docking results showed that the three residues in the ATR1 binding pocket (Phe162, Asp160, and Phe22) were essential for making hydrogen bond with the 2-(2-bromo-6-chloro-4H-purin-9(5H)-yl)- 5-(hydroxymethyl) tetrahydrofuran-3,4-diol (C(11)H(13)N(3)O(5)). The data presented here strongly indicate that the interactions of these four residues are necessary for a stronger binding of the ATR1 with C(11)H(13)N(3)O(5). Also, the study proposed C(11)H(13)N(3)O(5) as an effective inhibitor by the comparison of docking energy.
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Affiliation(s)
- Nitin K Singh
- Department of Environmental Biotechnology, Bharathidasan University, Tiruchirappalli, 620024, India
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29
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Berhanu WM, Ibrahim MA, Pillai GG, Oliferenko AA, Khelashvili L, Jabeen F, Mirza B, Ansari FL, ul-Haq I, El-Feky SA, Katritzky AR. Similarity analysis, synthesis, and bioassay of antibacterial cyclic peptidomimetics. Beilstein J Org Chem 2012; 8:1146-60. [PMID: 23019443 PMCID: PMC3458733 DOI: 10.3762/bjoc.8.128] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 06/01/2012] [Indexed: 12/04/2022] Open
Abstract
The chemical similarity of antibacterial cyclic peptides and peptidomimetics was studied in order to identify new promising cyclic scaffolds. A large descriptor space coupled with cluster analysis was employed to digitize known antibacterial structures and to gauge the potential of new peptidomimetic macrocycles, which were conveniently synthesized by acylbenzotriazole methodology. Some of the synthesized compounds were tested against an array of microorganisms and showed antibacterial activity against Bordetella bronchistepica, Micrococcus luteus, and Salmonella typhimurium.
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Affiliation(s)
- Workalemahu M Berhanu
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Mohamed A Ibrahim
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig-44519, Egypt
- Department of Organic Chemistry, College of Pharmacy, Misr University for Science and Technology, Al-Motamayez District, P.O. Box: 77, Egypt
| | - Girinath G Pillai
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Alexander A Oliferenko
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Levan Khelashvili
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | - Farukh Jabeen
- Department of Chemistry, Quaid i Azam University, Islamabad 45320, Pakistan
| | - Bushra Mirza
- Department of Biochemistry, Quaid i Azam University, Islamabad 45320, Pakistan
| | | | - Ihsan ul-Haq
- Department of Biochemistry, Quaid i Azam University, Islamabad 45320, Pakistan
| | - Said A El-Feky
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig-44519, Egypt
| | - Alan R Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
- Department of Chemistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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30
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Berhanu WM, Pillai GG, Oliferenko AA, Katritzky AR. Quantitative Structure-Activity/Property Relationships: The Ubiquitous Links between Cause and Effect. Chempluschem 2012. [DOI: 10.1002/cplu.201200038] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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31
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Zhong M, Jang M, Oliferenko A, Pillai GG, Katritzky AR. The SOA formation model combined with semiempirical quantum chemistry for predicting UV-Vis absorption of secondary organic aerosols. Phys Chem Chem Phys 2012; 14:9058-66. [DOI: 10.1039/c2cp23906j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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32
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Ha K, Monbaliu JCM, Williams BC, Pillai GG, Ocampo CE, Zeller M, Stevens CV, Katritzky AR. A convenient synthesis of difficult medium-sized cyclic peptides by Staudinger mediated ring-closure. Org Biomol Chem 2012; 10:8055-8. [DOI: 10.1039/c2ob25996f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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