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Scientific Articles

Broadly, I have worked and published my findings under the following research topics:

  1. Molecular modeling and simulation studies of various biological systems and compounds

  2. Development and characterization of chemosensors and fluorescent liquid crystals for bio-imaging applications

  3. Computational studies on potential drug candidates for various diseases including SARS-CoV-2, dengue, and malaria

  4. Investigations into the structural motifs of macrocyclic compounds for molecular recognition

  5. Molecular insights into selective recognition of linear peptide motifs by tandem BRCT domains

  6. Molecular modeling studies for structural and functional characterization of CXCR4 receptor-ligand interactions in HIV-1 infection

2021-22

  1. Athar, M., S. Gervasoni, A. Catte et al (2022). Tripartite efflux pumps of the RND superfamily: what did we learn from computational studies? Microbiology XX (Submitted)

  2. Vora, M., Panchal, M., Dey, S., Pandya, A., Athar, M., Verma, N., Jain, V. (2022). Oxacalix [4] arene based dual-signalling fluorimetric and electrochemical chemosensor for the selective detection of nitroaromatic compounds. 362, 119791

  3. Kongor, A., Athar, M., Vora, M., Bhatt, K., & Jain, V. (2022). Recent Developments on the Removal of Antibiotics Using Carbon-Based Nanocomposites: A Mystic Approach in Nanoscience. 255-273.

  4. Parmar, M., Thumar, R., Patel, B., Athar, M., Jha, P. C., & Patel, D. (2022). Structural differences in 3C-like protease (Mpro) from SARS-CoV and SARS-CoV-2: molecular insights revealed by Molecular Dynamics Simulations. Structural Chemistry.

  5. Athar, M., Kongor, A., Patel, D., Irfan, A., & Bhatt, K. (2022). Recent Development of Macrocyclic Compounds as Potential Tool for Cancer Therapy and Diagnosis: A Mini. volume 13, Issue 3, 2023, 252

  6. Rathod, S. L., Sharma, V. S., Sharma, A. S., Athar, M., Shrivastav, P. S., & Parekh, H. M. J. J. o. M. S. (2022). Blue light-emitting Quinoline armed Thiacalix [4] arene 3D-scaffold: a Systematic Platform to construct Fluorescent Liquid Crystals with Bio-imaging Applications. 133830.

  7. Sharma, V. K., Patel, U., Thakar, S., Rathod, S. L., Sharma, A., Shrivastav, P. S., & Athar, M. (2022). Fluorescein appended calixarene functionalized supramolecular AIE-active liquid crystalline materials for self-assembly and bio-imaging applications. New Journal of Chemistry. doi:10.1039/D2NJ05133H

  8. Athar, M., & Patnaik A. (2022). Through-Bond Driven Through-Space Interactions in a Fullerene C60 Non-Covalent Dyad: Unusual Strong Binding between Spherical and Planar π Electron Clouds and Culmination of Dyadic Fractals. The Journal of Physical Chemistry A.  126, 23, 3629–3641

  9. Patel, D., Athar, M., & Jha, P. C. (2022). Computational investigation of binding of chloroquinone and
    hydroxychloroquinone against PLPro of SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 40(7), 3071-3081.

2020-2015

  1. Athar, M. Vadiraj K. Bharatham K. (2020), Molecular Insights into Selective Recognition of Phosphorylated Linear Peptide Motifs by Tandem BRCT Domains. Proceedings of International Conference on Drug Discovery (ICDD). Full paper yet to come

  2. Patel, D.#, Athar, M. #, & Jha, P. C. (2021). Exploring Ruthenium-based organometallic inhibitors against Plasmodium Calcium Dependent Kinase 2 (PfCDPK2): a combined ensemble docking, QM/MM and molecular dynamics study. ChemistrySelect. 6, 32, 8189-8199. Equal Contribution

  3. Vora, M., Kongor, A., Panchal, M., Athar, M., Verma, A., Panjwani, & Jain, V. (2020). A highly selective anthraquinone appended oxacalixarene receptor for fluorescent ICT sensing of F- ions: an experimental and computational study. Journal of Chemical Sciences, 132(1), 1-10.

  4. Vora, J., Patel, S., Athar, M., Sinha, S., Chhabria, M. T., Jha, P. C., & Shrivastava, N. (2020). Pharmacophore modeling, molecular docking and molecular dynamics simulation for screening and identifying anti-dengue phytocompounds. J Biomol Struct Dyn, 38(6), 1726-1740.

  5. Vora, J., Athar, M., Sinha, S., Jha, P. C., & Shrivastava, N. (2020). Binding Insight of Anti-HIV Phytocompounds with Prime Targets of HIV: A Molecular Dynamics Simulation Analysis. Curr HIV Res, 18(2), 132-141

  6. Panchal, M., Kongor, A., Athar, M., Modi, K., Patel, C., Dey, S., Jain, V. K. (2020). Structural motifs of oxacalix[4]arene for molecular recognition of nitroaromatic explosives: Experimental and computational investigations of host-guest complexes. Journal of Molecular Liquids, 306, 112809

  7. Kongor, A., Panchal, M., Athar, M., Vora, M., Verma, N., Pandya, A., Jain, V. (2020). Colorimetric and electrochemical sensing of As(III) using calix[4]pyrrole capped gold nanoparticles and evaluation of its cytotoxic activity. Journal of Inclusion Phenomena and Macrocyclic Chemistry, 98(1-2), 29-41

  8. Kongor, A., Panchal, M., Athar, M., Vora, M., Makwana, B., Jha, P. C., & Jain, V. (2020). Calix[4]pyrrole Stabilized PdNPs as an Efficient Heterogeneous Catalyst for Enhanced Degradation of Water-Soluble Carcinogenic Azo Dyes. Catalysis Letters, 151(2), 548-558.

  9. Athar, M., Behzadi, H., & Makki, S. (2020). Understanding non‑covalent interactions by NMR in urea‑and thiourea‑substituted calixarene complexes. MONATSHEFTE FUR CHEMIE, 151(5), 743-749.

  10. Kongor, A., Panchal, M., Athar, M., Bhatt, K., Jha, P. C., & Jain, V. (2019). Facile construction of calix [4] pyrrole-templated gold nanoparticles: computational insights and application for efficient reduction of 4-nitrophenol. Gold Bulletin, 52(3-4), 125-133.

  11. Patel, S. K., Athar, M., Jha, P. C., Khedkar, V. M., Jasrai, Y., Pandya, H. A., Sharma, S. (2019). Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations. Letters in Drug Design & Discovery, 16(3), 291-300

  12. Athar, M., Das Soubhik, Jha PC et al., (2018). Conformational Equilibrium Study of Calix[4]tetrolarenes using Density Functional Theory (DFT) and Molecular Dynamics Simulations, Supramolecular Chemistry. 30, 12, 982-993

  13. Athar, M., & Jha, P. C. (2019) DFT study of guest-responsive cooperative effects: Inclusion complexation of alcohols with calix[4]pyrrole, Monatshefte für Chemie - Chemical Monthly. 150, (7) 1205–1214 -This work describes molecular assembly behaviours and long-range cooperative effects that are mainly encoded by the charge polarising effects.

  14. Sharma, V. S., Sharma, A. S., Shah, A. P., Shah, P. A., Shrivastav, P. S., & Athar, M. (2019). New Class of Supramolecular Bowl-Shaped Columnar Mesogens Derived from Thiacalix [4] arene Exhibiting Gelation and Organic Light-Emitting Diodes Applications. ACS omega, 4(14), 15862-15872.

  15. Sinha, S., Patel, S., Athar, M., Vora, J., Chhabria, M.T., Jha, P.C. and Shrivastava, N., (2019). Structure-based identification of novel sirtuin inhibitors against triple negative breast cancer: An in silico and in vitro study. International journal of biological macromolecules. 140, 454-568.

  16. Shah, D. J., Sharma, A. S., Shah, A. P., Sharma, V. S., Athar, M., & Soni, J. Y. (2019). Fixation of CO2 as a carboxylic acid precursor by microcrystalline cellulose (MCC) supported Ag NPs: a more efficient, sustainable, biodegradable and eco-friendly catalyst. New Journal of Chemistry, 43(22), 8669-8676.

  17. Athar, M., Ranjan, P., & Jha, P. C. (2018). A DFT study of inclusion complexes of substituted calix[n]arenes with dasatinib and lapatinib. Journal of molecular graphics & modelling, 84, 160-165 -Variety of complexes were appraised to approximate the real geometry. I have utilized range of computational methods to achieve the converged structure. Such methodology will be helpful to model challenging complexation problems.

  18. Sharma, V. S., Shah, A. P., Sharma, A. S., & Athar, M. (2019). Columnar self-assembly, gelation and electrochemical behavior of cone-shaped luminescent supramolecular calix[4]arene LCs based on oxadiazole and thiadiazole derivatives. New Journal of Chemistry, 43(4), 1910-1925.

  19. Ranjan, P., Athar, M., Vijayakrishna, K., Meena, L. K., Vasita, R., & Jha, P. C. (2018). Deciphering the anthelmintic activity of benzimidazolium salts by experimental and in-silico studies. Journal of Molecular Liquids, 268, 156-168

  20. Ranjan, P., Athar, M., Rather, H., Vijayakrishna, K., Vasita, R., & Jha, P. C. (2018). Rational design of imidazolium based salts as anthelmintic agents. Journal of Molecular Liquids, 255, 578-588.

  21. Ranjan, P., Athar, M., Rather, H., Vijayakrishna, K., Vasita, R., & Jha, P. C. (2018). Appraisal of 1‐Butylimidazole‐Derived Ionic Liquids as Anthelmintic Agents: An Experimental and In Silico Approach. ChemistrySelect, 3(26), 7518-7526.

  22. Kongor, A., Panchal, M., Athar, M., Mehta, V., Bhatt, K., Jha, P. C., & Jain, (2018) Synthesis and modeling of calix[4]pyrrole wrapped Au nanoprobe for specific detection of Pb(II): Antioxidant and radical scavenging efficiencies, Journal of Photochemistry and Photobiology A: Chemistry. 364, 801-810.

  23. Ranjan, P., Athar, M., Vijayakrishna, K., & Jha, P. C. (2018). Probing the opportunities for designing Anthelmintic leads by Sub-Structural Topology Based QSAR Modelling. Molecular Diversity 22 (3), 669-683. -Developed 2D-QSAR model for enriched tubulin inhibitors retrieved from sequence similarity and applicability domain searches.

  24. Kongor, A., Panchal, M., Athar, M., Mehta, V., Bhatt, K., Jha, P. C., & Jain, V. (2018). Heterogeneous hydrogenation using stable and reusable calix [4] pyrrole fenced Pt nanoparticles and its mechanistic insight. 437, 195-201. Applied Surface Science.

  25. Athar, M., Lone, M. Y., & Jha, P. C. (2017). Recognition of Anions using urea and thiourea substituted calixarenes: A DFT assessment of Non-Covalent Interactions. Chemical Physics 501, 68-7.

  26. Lone, M. Y., Manhas, A., Athar, M., & Jha, P. C. (2018). Identification of InhA inhibitors: A combination of virtual screening, molecular dynamics simulations and quantum chemical studies. J Biomol Struct Dyn, 36(11), 2951-2965

  27. Athar, M., Lone, M. Y., & Jha, P. C. (2018). Designing of Calixarene based Drug Carrier for Dasatinib, Lapatinib and Nilotinib using Multilevel Molecular Docking, Semiemperical and Dynamics Simulations, Journal of Inclusion Phenomena and Macrocyclic Chemistry. 90, 157-169.

  28. Mehta, V., Athar, M., Jha, P. C., Kongor, A., Panchal, M., & Jain, V. K. (2017). A turn-off fluorescence sensor for insensitive munition using anthraquinone-appended oxacalix[4]arene and its computational studies. New Journal of Chemistry, 41(12), 5125-5132

  29. Athar M, K. A., Panchal M, Jha PC, Jain V. (2017). Entrapment of Toxic Anions using Calixarenes Framework. MOJ Toxicology, 3(6)

  30. Kongor, A., Panchal, M., Athar, M., Jha, P. C., Jhala, D., Sindhav, G., Jain, V. K. (2018). Selective fluorescence sensing of Cu(II) ions using calix[4]pyrrole fabricated Ag nanoparticles: A spectroscopic and computational approach. Journal of Molecular Liquids, 269, 467-475

  31. Lone, M. Y., Athar, M., Kumar, S.P., & Jha, P. C. (2017) Exploration of Mycobacterium tuberculosis Structural Proteome: An In-silico Approach. Journal of Theoretical Biology 439, 14-23. -Multiple complex-based pharmacophore and hypotheses screening was performed for whole Mycobacterium proteome. Later, as a proof of concept, two targets (InhA, enoyl-acyl carrier protein reductase) were screened for small molecules and tested by invitro experiments.

  32. Lone, M. Y., Athar, M., Manhas, A., Jha, P. C., Bhatt, S., & Shah, A. (2017). In Silico Exploration of Vinca Domain Tubulin Inhibitors: A Combination of 3D-QSAR-Based Pharmacophore Modeling, Docking and Molecular Dynamics Simulations. ChemistrySelect, 2(33), 10848-10853

  33. Panchal, M. K., Kongor, A., Athar, M., Mehta, V. A., Jha, P. C., Jain, V. K., (2017). Sensing of Ce(III) using di-naphthoylated oxacalix[4]arene via realistic simulations and experimental studies. New Journal of Chemistry. 42, 311-31.

  34. Athar, M., Lone, M. Y., & Jha, P. C. (2017). Investigation of structure and conformational equilibrium of Oxacalix [4] arene: A density functional theory approach. Journal of Molecular Liquids. 237, 473-483. -We determined that the 1,3-alternate conformer was relatively more stable due to the presence of bridged oxygen that strengthen the cation pi and pi-pi interactions in oxacalix[4]arene.

  35. Panchal, M., Athar, M., Jha, P. C., Kongor, A., Mehta, V., & Jain, V. (2017). Quinoline appended oxacalixarene as turn-off fluorescent probe for the selective and sensitive determination of Cu2+ ions: A combined experimental and DFT study. Journal of Luminescence, 192, 256-262.

  36. Lone, M. Y., Athar, M., Gupta, V. K., & Jha, P. C. (2017). Identification of Mycobacterium tuberculosis enoyl-acyl carrier protein reductase inhibitors: A combined in-silico and in-vitro analysis. J Mol Graph Model, 76, 172-180

  37. Athar, M., Lone, M. Y., & Jha, P. C. (2017). First protein drug target's appraisal of lead-likeness descriptors to unfold the intervening chemical space. J Mol Graph Model, 72, 272-282.

  38. Athar, M., Lone, M. Y., Khedkar, V. M., Radadiya, A., Shah, A., & Jha, P. C. (2017). Structural Investigation of Vinca Domain Tubulin Binders by Pharmacophore, Atom based QSAR, Docking and Molecular Dynamics Simulations. Comb Chem High Throughput Screen, 20(8), 682-695

  39. Lone, M. Y., Athar, M., Gupta, V. K., & Jha, P. C. (2017). Prioritization of natural compounds against mycobacterium tuberculosis 3-dehydroquinate dehydratase: A combined in-silico and in-vitro study. Biochem Biophys Res Commun, 491(4), 1105-1111

  40. Athar, M., Lone, M. Y., & Jha, P. C. (2017). Theoretical assessment of calix[n]arene as drug carriers for second generation tyrosine kinase inhibitors, Journal of Molecular Liquids, 247, 448-455.

  41. Athar, M., Lone, M. Y., Khedkar, V. M., & Jha, P. C. (2016). Pharmacophore model prediction, 3D-QSAR and molecular docking studies on vinyl sulfones targeting Nrf2-mediated gene transcription intended for anti-Parkinson drug design. Journal of Biomolecular Structure and Dynamics, 34(6), 1282-1297.

  42. Panchal, M., Athar, M., Jha, P. C., Kongor, A., Mehta, V., Bhatt, K., & Jain, V. K. (2016). Turn-off fluorescence probe for the selective determination of pendimethalin using a mechanistic docking model of novel oxacalix [4] arene. RSC Advances, 6(58), 53573-53577.

  43. Mehta, V., Athar, M., Jha, P. C., Panchal, M., Modi, K., & Jain, V. K. (2016). Efficiently functionalized oxacalix [4] arenes: Synthesis, characterization and exploration of their biological profile as novel HDAC inhibitors. Bioorganic & medicinal chemistry letters, 26(3), 1005-1010.

  44. Athar, M., & Das, A. J. (2014). Therapeutic nanoparticles: State-of-the-art of nanomedicine. Adv. Mater. Rev, 1(1), 25-37.

Research monographs/Book-Chapters

  • Athar M, Sona AM, Bekono BD, Fidele NK; (2019), Fundamental physical and chemical concepts behind "drug-likeness" and "natural product-likeness". Cheminformatics of Natural Products, Physical Sciences Reviews. 55-80. DeGruyter. ISBN 978-3110579338

  • Koulouridi E, Athar M. et al, (2019) Glossary of terms used in chemoinformatics of natural products: fundamental principles. In Volume 1 Fundamental Concepts (pp. 417-442). De Gruyter.

  • Kongor A, Panchal M, Athar M, Jain VK, (2019) Calix- Assisted Fabrication of Metal Nanoparticle s: Applications and Theoretical Insights, 21st Century Nanoscience – A Handbook (Volume 2). Taylor Francis 15-1, 15-14. eBook ISBN9780367341558

  • Kongor A, Athar M, Vora M, Bhatt K and Jain V, 2022, Recent Developments on the Removal of Antibiotics Using Carbon-Based Nanocomposites: A Mystic Approach in Nanoscience, Novel Applications of Carbon-Based Nano-Materials, CRC Press

The papers cover a wide range of topics related to molecular modeling and simulation studies, computational studies on potential drug candidates, and the development of chemosensors and fluorescent liquid crystals for bio-imaging applications. Many of the studies focus on the development of potential treatments for various diseases including SARS-CoV-2, dengue, and malaria. Additionally, there are investigations into the structural motifs of macrocyclic compounds for molecular recognition and molecular insights into selective recognition of linear peptide motifs by tandem BRCT domains. One paper also focuses on the molecular modeling studies for structural and functional characterization of CXCR4 receptor-ligand interactions in HIV-1 infection.

Conformational equilibrium study of calix[4]tetrolarenes using Density Functional Theory (DFT) and Molecular Dynamics simulations

Sep 10, 2018​

The present work deals with the theoretical study of conformational equilibrium of calix[4]tetrolarenes (1,2,3 trimethoxy substituted calix[4]arene) in gaseous and solvation phases. A total of 64 calculations (four conformations at eight level of theories) were performed using Density Functional Theory (DFT) functionals viz. wB97XD, B97D, B3LYP, CAM-B3LYP with diffused (6–31 + G(d)) and non-diffused basis sets (6-31G(d)). It has been found that the conformational profile of calix[4]tetrolarene changes from cone to 1,3-Alternate upon incorporating – OMe group. The B97D and wB97XD functionals gave the most accurate result having rmsd value ~0.73Å followed by B3LYP and CAM-B3LYP > 0.78Å. Furthermore, NBO calculations demonstrated that reduction in charges at lower rim oxygens reduces the chances of hydrogen bonding. Moreover, global reactivity parameters and molecular dynamics also complement the observed trend. Owing to the methoxy substitutions, anion binding study of these new molecules indicates towards the promising capability to bind Cl− and F− ions.

Sensing of Ce(III) using di-naphthoylated oxacalix[4]arene via realistic simulations and experimental studies

Dec 20, 2017

Here, we report a fluorescent sensor for the detection of Ce(III) using di-naphthoylated oxacalix[4]arene (DNOC). Formation of the DNOC-Ce(III) complex has been confirmed by 1H NMR and mass spectroscopic observations. A dramatic decrease in the emission intensity of DNOC is observed for Ce(III) with no competitive interference due to other divalent and trivalent ions. The linear range of detection was obtained over a concentration range between 18 nM and 2 μM. Furthermore, density functional theory (DFT)-based quantum mechanical calculations were executed to predict the most probable structure of the host–guest system. As the molecular geometry suggests, the nitro groups of DNOC bent and the naphthoyl groups (oxygen centres of alternate calixarene rings) stabilize the cerium inclusion complex in the 1,3-alternate conformation. Thus, a novel analytical approach has been developed for Ce(III) detection using the oxacalixarene framework in solution. Moreover, the selective behaviour of DNOC also facilitates new opportunities for determining Ce(III) in a wide range of real samples

Designing of calixarene based drug carrier for dasatinib, lapatinib and nilotinib using multilevel molecular docking and dynamics simulations

April, 04, 2018

Herein, an in-silico attempt was made to improve the pharmacological profile of second generation tyrosine kinase inhibitors (TKI’s) viz. dasatinib, lapatinib and nilotinib by forming their host–guest inclusion complexes with calixarene. We have investigated the energetics and binding behaviour of TKI’s with upper rim functionalised calix[n]arenes (n = 4,5,6 and 8) via appended groups (R=SO3H, tert-Butyl, iso-Propyl, COOH, C2H5OH, and C2H5NH2). For this, multilevel molecular docking approach with shape based fitting algorithms (Patchdock/Firedock and HexServer) followed by semiemperical PM3 calculations were employed to generate structural mode of complexes. Further, based on interaction energies and their structural integrity (dynamics behaviour), we concluded that the proposed drug carrier (host) for nilotinib (C2H5SO3H-calix[4]arene, and isopropyl/C2H5NH2-calix[8]arene), dasatinib (C2H5SO3H-calix[5]arene, C2H5COOH-calix[6]arene, tert-butyl-calix[6]arene) and lapatinib (C2H5SO3H/C2H5COOH-calix[6]arene and C2H5COOH-calix[8]arene) have the greater capability to form optimal complexes.

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