Publications

2024

Structural studies of catalytic peptides using molecular dynamics simulations. Parth Rathee, Sreerag N. Moorkkannur, and Rajeev Prabhakar. Methods in Enzymology, 2024, In press. DOI: https://doi.org/10.1016/bs.mie.2024.01.019.

2023 

Application of Molecular Dynamic Simulations in Modeling the Excited State Behavior of Confined Molecules.; Dipendra Khadka; Vindi M Jayasinghe-Arachchige; Rajeev Prabhakar and Vaidhyanathan Ramamurthy. Photochemical & Photobiological Sciences, 2023, In press. DOI: https://doi.org/10.1007/s43630-023-00486-2  

Modeling of orange carbon dots-CO2 interaction and its effects on photosynthesis and productivity in maize and green beans. Milenković, Ivana; Zhou, Yiqun; Borišev, Milan; Serafim, Leonardo;  Chen, Jiuyan; ElMetwally, Ahmed; Spasić, Sladjana; Algarra, Manuel; Martinez de Yuso, M.V.; Prabhakar, Rajeev; Leblanc, Roger; Radotic, Ksenija. Journal of Environmental Informatics, 2023. In press.

Discovery of SARS-CoV-2 inhibitors featuring novel histidine α-nitrile motif. Nilu V. Gone, Ghalib Mohammed, Jessy Thomas, Parth Rathee, Rajeev Prabhakar, Kiran K. Bokara, Gangadhar J. Sanjayan. Chemistry and Biodiversity, 2023, in press. DOI: https://doi.org/10.1002/cbdv.202300957

Feature article: Investigating Roles of Distinct Chemical Factors in Hydrolytic Reactions Catalyzed by Metalloenzymes and Metal Complexes. Serafim, Leonardo; Jayasinghe-Arachchige Vindi; Wang, Lukun; Rathee, Parth; Yang, Jiawen; Sreerag N. Moorkkannur; and Prabhakar, Rajeev. Chem Commun, 2023, 59, 8911-8928. DOI: https://doi.org/10.1039/D3CC01380D.

Elucidating the Roles of Distinct Chemical Factors in the Hydrolytic Activities of Hetero- and Homonuclear Synthetic Analogues of Binuclear Metalloenzymes. Jayasinghe-Arachchige, Vindi; Serafim, Leonardo; Hu, Qiaoyu; Ozen, Cihan; Sreerag N. Moorkkannur; Schenk, Gerhard; Prabhakar, Rajeev. ACS Catalysis, 2023, 13, 3131–3147. DOI: https://pubs.acs.org/doi/10.1021/acscatal.2c05758

In vitro anti-Leishmania activity of new isomeric cobalt(II)complexes and in silico insights: mitochondria impairment and apoptosis-like cell death of the parasite. Samuel M. Rocha , Adolfo Horn Jr, Aline R. de M. L. Terra, Lara M. Rezende, Felipe F. Moreira, Renato A. DaMatta, Fernando R. Xavier, Rodrigo Cervo, Roberta Cargnelutti, Sreerag N. Moorkkannur, Graysen Owenby, Rajeev Prabhakar, Sérgio H. Seabra, Christiane Fernandes. Journal of Inorganic Biochemistry, 2023, 240, 112088. DOI:https://doi.org/10.1016/j.jinorgbio.2022.112088

Deconvoluting Amyloid Aggregation Using Photoluminescence Lifetime: a hidden binding site revealed. Bo Jiang, Utana Umezaki, Andrea Augustine, Vindi M. Jayasinghe‐Arachchige, Leonardo F. Serafim, Kevin M. Wyss, Rajeev Prabhakar, Angel A. Martí. Chemical Science, 2023, 14, 1072-1081. DOI: https://doi.org/10.1039/D2SC05418C (Also contributed cover art for the issue).

2022   

Carbon Dot Nanoarchitectonics: Quadruple conjugated nano model for superior cancer cell-nucleus targeting and multi drug delivery. Emel Kirbas Cilingir; Sajini D. Hettiarachchi; Parth Rathee; Yiqun Zhou; Arya Ajith; Braulio CLB Ferreira; Lukun Wang; Rajeev Prabhakar; Steven Vanni; Roger M. Leblanc; Regina M. Graham. Carbon, 2022, submitted.

Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses. Leonardo F. Serafim, Vindi M. Jayasinghe-Arachchige, Lukun Wang, and Rajeev Prabhakar. Journal of Chemical Information and Modeling, 2022, 62, 10, 2466–2480. DOI: https://doi.org/10.1021/acs.jcim.2c00214 

Organic Host Encapsulation Effects on Nitrosobenzene Monomer-Dimer Distribution and C-NO Bond Rotation in Aqueous Solution. Varadharajan, Ramkumar ; Kelley, Sarah; Jayasinghe-Arachchige, Vindi ; Prabhakar, Rajeev; Ramamurthy, Vaidhyanathan; Blackstock, Silas. ACS Org. Inorg. Au 2022, 2, 2, 175–185. DOI: https://doi.org/10.1021/acsorginorgau.1c00043

Structure-Activity Relationship of Carbon Nitride Dots in Inhibiting Tau Aggregation. Yiqun Zhou, Nabin Kandel, Mattia Bartoli, Leonardo Farias Serafim, Ahmed E. El Metwally, Sophia M. Falkenberg, Xavier E. Paredes, Christopher J. Nelson, Nathan Smith, Elisa Padovano, Wei Zhang, Keenan J. Mintz, Braulio C.L.B. Ferreira, Emel Kirbas Cilingir, Jiuyan Chen, Sujit K. Shah, Rajeev Prabhakar, Alberto Tagliaferro, Chunyu Wang and Roger Leblanc. Carbon, 2022, 193, 1-16. DOI: https://doi.org/10.1016/j.carbon.2022.03.021 

Peptide hydrogel with self-healing and redox-responsive properties. Areetha D’Souza, Liam R. Marshall, Jennifer Yoon, Alona Kulesha, Siddarth Chandrasekaran, Dona I.U. Edirisinghe, Parth Rathee, Rajeev Prabhakar and Olga Makhlynets. Nano Convergence, 2022, 9(1), 1-8. DOI: https://doi.org/10.1186/s40580-022-00309-7 

2021 

Interacctions of Urea-based Inhibitors with Prostate-Specific Membrane Antigen (PSMA) for Boron Neutron Capture Therapy (BNCT). Qiaoyu Hu, Kevin Padron, Daiki Hara, Junwei Shi, Alan Pollack, Rajeev Prabhakar and Wensi Tao. ACS Omega, 2021, 6, 49, 33354–33369. DOI: https://doi.org/10.1021/acsomega.1c03554 

Remediation of Environmentally Hazardous Organophosphates by Artificial Metalloenzymes. Leonardo F. Serafim, Lukun Wang, Parth Rathee, Jiawen Yang, Hannah Sofia Frenk Knaul and Rajeev Prabhakar. Current Opinion in Green and Sustainable Chemistry, 2021, 32, 100529. DOI: https://doi.org/10.1016/j.cogsc.2021.100529

Dynamics of Anthracene Excimer Formation within a Water-soluble Nanocavity at Room Temperature. Das, Aritra; Danao, Ashwini; Banerjee, Shubhojit; Mohan Raj, Anthony Raj; Sharma, Gaurav; Prabhakar, Rajeev; Srinivasan, Varadharajan; Ramamurthy, Vaidhyanathan; Sen, Pratik. Journal of the American Chemical Society, 2021, 143, 2025. DOI: https://doi.org/10.1021/jacs.0c12169

Degradation of a Main Plastic Pollutant Polyethylene Terephthalate (PET) by Two Distinct Proteases (Neprilysin and Cutinase-Like Enzyme). Qiaoyu Hu, Vindi Jayasinghe-Arachchige, Rajeev Prabhakar. Information and Modeling, 2021, 61, 2, 764. DOI: https://doi.org/10.1021/acs.jcim.0c00797 

2020 

Encapsulation Effects on Intermolecular Association and Intramolecuar Dynamics of Nitrosobenzenes in Aqueous Solution. Varadharajan, Ramkumar; Ariel Kelley, S.; Jayasinghe-Arachchige, Vindi; Prabhakar, Rajeev; Blackstock, Silas; Ramamurthy, Vaidhyanathan. Journal of the American Chemical Society Communication, 2020, Under Review.

Clavanin A is a Potent Antibacterial Agent against Multi-Drug Resistant Gram-Negative Pathogens – Insight into its Zn²⁺-Dependent Activity. Juliano S, Sharma G, Serafim L, Duay S, Chavez M, Comert F, Radulescu A, Cotton M, Mihailescu M, Eric R. May, Greenwood A, Prabhakar R, and Angeles-Boza A. ACS Infectious Diseases, 2020, 6, 5, 1250–1263, DOI: https://doi.org/10.1021/acsinfecdis.0c00051. (Link)

Mechanisms of peptide and phosphoester hydrolysis catalyzed by two promiscuous metalloenzymes (insulin degrading enzyme and glycerophosphodiesterase) and their synthetic analogues. Qiaoyu Hu, Vindi M. Jayasinghe-Arachchige, Gaurav Sharma, Leonardo F. Serafim, Thomas J. Paul and Rajeev Prabhakar, WIREs Computational Molecular Science, 2020; e1466, DOI:10.1002/wcms.1466. (Link) 

Developing Artificial Enzymes using Computers. Advanced Science News. Rajeev Prabhakar. (Link)

Heteromeric 3-Stranded Coiled Coils Designed Using a Pb(II)(Cys)₃ Template Mediated Strategy. Audrey E Tolbert, Catherine S Ervin, Leela Ruckthong_, Thomas J Paul_, Vindi M. Jayasinghe-Arachchige, Kosh P. Neupane, Jeanne A Stuckey, Rajeev Prabhakar, and Vincent L Pecoraro. Nature Chemistry. 2020, 0243-6. DOI:10.1038/s41557-020-0423-6. (Link) Highlighted in NEWS at TheU. (Link) 

Effect of Chemically Distinct Substrates on the Mechanism and Reactivity of a Highly Promiscuous Metallohydrolase. Gaurav Sharma, Vindi M. Jayasinghe-Arachchige,  Qiaoyu Hu, Gerhard Schenk and Rajeev Prabhakar. ACS Catalysis, 2020, 10, 3684-3696 DOI: doi.org/10.1021/acscatal.9b04847. (Link)

Deconvoluting Amyloid Aggregation using Photoluminescence Lifetime. Bo J, Vindi M. Jayasinghe-Arachchige, Serafim L, Wyss K, Andrea A, Prabhakar R, and Marti A. Angewandte Chemie International Edition, 2020, submitted.

 2019 

Advances in the Development of Artificial Metalloenzymes (E-book), Ed. Tatjana N. Parac-Vogt , Andrea Erxleben , Gerhard Schenk and Rajeev Prabhakar, Frontiers in Chemistry, 2019, DOI:10.3389/fchem.2019.00599. (Link)

Room Temperature Phosphorescence from Encapsulated Pyrene Induced by Xenon. Mohan Raj, A; Sharma, Gaurav; Prabhakar, Rajeev; Ramamurthy, Vaidhyanathan. The Journal of Physical Chemistry A. 2019, 123, 42, 9123-9131. DOI:https://doi.org/10.1021/acs.jpca.9b08354, (link)

Space constrained stereoselective geometric isomerization of 1,2-diphenylcyclopropane and stilbenes in an aqueous medium. Raj, A. Mohan; Sharma, Gaurav; Prabhakar, Rajeev; Ramamurthy, Vaidhyanathan. Organic Letters, 2019, 21, 13, 5243-5247. DOI:10.1021/acs.orglett.9b01176. (Link)

Ultrafast Solvation Dynamics Reveal the Octa Acid Capsule’s Interior Dryness Depends on the Guest. Das, Aritra; Sharma, Gaurav; Kamatham, Nareshbabu; Prabhakar, Rajeev; Sen, Pratik; Ramamurthy, Vaidhyanathan, The Journal of Physical Chemistry A. 2019, 123, 28, 5928-5936. DOI:10.1021/acs.jpca.9b04626. (Link)

Ultrafast Trans → Cis Photoisomerization Dynamics of Alkyl-Substituted Stilbenes in a Supramolecular Capsule. Otolski, Christopher; Raj, A. Mohan; Sharma, Gaurav; Prabhakar, Rajeev; Ramamurthy, Vaidhyanathan; Elles, Christopher. The Journal of Physical Chemistry A. 2019, 123, 24, 5061-5071. DOI:10.1021/acs.jpca.9b03285. (Link)

Molecular Dynamics Investigation into the Effect of Zinc(II) on the Structure and Membrane Interactions of the Antimicrobial Peptide Clavanin A. Searle Duay, Gaurav Sharma, Rajeev Prabhakar, Alfredo Angeles-Boza, and Eric May. The Journal of Physical Chemistry B. 2019, 123, 3163-3176. DOI: 10.1021/acs.jpcb.8b11496. (Link)

Effects of the Metal Ion on the Mechanism of Phosphodiester Hydrolysis Catalyzed by Metal-Cyclen Complexes. Qiaoyu Hu, Vindi M. Jayasinghe-Arachchige, Joshua Zuchniarz and Rajeev Prabhakar. Frontiers in Chemistry. 2019, 7: 195. DOI: 10.3389/fch-em.2019.00195. (Link).

Investigating Coordination Flexibility of Glycerophosphodiesterase (GpdQ) Through Interactions with Mono-, Di-, and Triphosphoester (NPP, BNPP, GPE, and Paraoxon) Substrates. Gaurav Sharma, Qiaoyu Hu, Vindi M. Jayasinghe-Arachchige,  Thomas Paul, Gerhard Schenk and Rajeev Prabhakar. Physical Chemistry Chemical Physics. 2019, 21, 5499-5509. DOI: 10.1039/C8CP07031H. (Link)

2018    

Investigating Polyoxometalate-Protein Interactions at Chemically Distinct Binding Sites. Thomas J. Paul, Tatjana Parac-Vogt, David Quiñonero, Rajeev Prabhakar. The Journal of Physical Chemistry B. 2018, 122 (29), 7219–7232. DOI: 10.1021/acs.jpcb.8b02931 (Link)

Hydrolysis of Chemically Distinct Sites of Human Serum Albumin (HAS) by Polyoxometalate (POM): A Hybrid QM/MM (ONIOM) Study. Vindi M. Jayasinghe-Arachchige, Qiaoyu Hu, Gaurav Sharma, Thomas J. Paul, Marcus Lundberg, David Quiñonero, Tatjana N. Parac-Vogt and Rajeev Prabhakar. Journal of Computational Chemistry. 2018. DOI: 10.1002/jcc.25528 (Link)

Formation of Catalytically Active Binuclear Center of Glycerophosphodiesterase (GpdQ): A Molecular Dynamics Study. Thomas J. Paul, Gerhard Schenk, Rajeev Prabhakar. The Journal of Physical Chemistry B. 2018, 122 (22), 5797–5808, DOI: 10.1021/acs.jpcb.8b02046 (Link)

2017

Photochemical Identification of Molecular Binding Sites  on the Surface of Amyloid-β Fibillar Aggregrates. Amir Aliyan, Thomas J. Paul, Christopher Pennington, Gaurav Sharma, Rajeev Prabhakar, Angel Martí. Chem. 2017, 3, 898-912. DOI: http://dx.doi.org/10.1016/j.chempr.2017.09.011 (Link)

Structural and Mechanistic Insights into Development of Chemical Tools to Control Individual and Inter-related Pathological Features in Alzheimer’s Disease. Hyuck Jin Lee, Kyle J. Korshavn, Younwoo Nam, Juhye Kang, Thomas J. Paul, Richard A. Kerr, Il Seung Youn, Mehmet Ozbil, Kwang S. Kim, Brandon T. Ruotolo, Rajeev Prabhakar, Ayyalusamy Ramamoorthy and Mi Hee Lim. Chemistry - A European Journal. 2017, 23, 2706-15 DOI: 10.1002/chem.201605401 (Link)

Effects of Ligand Environment in Zr(IV) Assisted Peptide Hydrolysis. Zhang, Tingting; Sharma, Gaurav ; Paul, Thomas; Hoffmann, Zachary; Prabhakar, Rajeev. Journal of Chemical Information and Modeling. 2017, 57.5, 1079-1088. DOI: 10.1021/acs.jcim.6b00781 (Link)

CD11b Activation Suppresses TLR-Dependent Inflammation and Autoimmunity in Systemic Lupus Erythematosus. Faridi M, Khan S, Zhao W, Zhang K, Kumar V, Armstrong A R, Moore E, Dorschner J M, Schnaith A M, Purmalek M, Carmona-Rivera C, Irizarry-Caro J, Zhang T, Day R, Stoub D, Hoffman V, Jehangir S, Bhargava P, Lopez A, Torroella-Kouri M, Isaac B, Altintas M A, Cimbaluk D, Zloza A, Prabhakar R, Deep S, Jolly M, Koh K H, Lee H W, Reichner J, Bradshaw E, Chen J, Moita L, Yuen P, Tsai W, Niewold T, Vazquez-Padron R, Kaplan M, and Gupta V. The Journal of clinical investigation 127.4, 2017: 1271-1283.  DOI: 10.1172/JCI88442 (Link)

2016

Cooperative Self-assembly of a Quaternary Complex Formed by Two Cucurbit[7]uril Hosts, Cyclobis(paraquat-p-phenylene) and a “Designer” Guest. Mohammad Hossein Tootoonchi, Gaurav Sharma, Jonathan Calles, Rajeev Prabhakar and Angel E. Kaifer. Angewandte Chemie. 2016, 55, 1-6. DOI: 10.1002/anie.201606038R1 (Link)

Design of Heparin Based Molecules for Inhibition of Alzheimer Amyloid Beta (Aβ40) Aggregation. Thomas J. Paul, Harvey Kelly, Joshua Zuchniarz, Tahir Ahmed and Rajeev Prabhakar. Canadian Journal of Chemistry. 2016, DOI: 10.1139/cjc-2016-0292 (Link)

Structural and Mechanical Properties of Amyloid Beta Fibrils: A Combined Experimental and Theoretical Approach. Thomas J. Paul, Zachary Hoffmann, Congzhou Wang, Maruda Shanmugasundaram, Jason DeJoannis, Alexander Shekhtman, Igor K. Lednev, Vamsi K. Yadavalli, and Rajeev Prabhakar. Journal of Physical Chemistry Letters. 2016, 7, 2758–2764. (Link)

Mechanisms of Peptide Hydrolysis by Aspartyl and Metalloproteases. Paul T J, Bora R, Ozbil M, Zhang T, Barman, A, Sharma, G, Hoffmann, Z and Prabhakar R. Phys Chem Chem Phys (PCCP), 2016. DOI: 10.1039/C6CP02097F (Link)

Structural and Material Properties of Amyloid Fibrils. Dong M, Paul T, Hoffmann Z, Chan K, Hu D, Ai H, and Prabhakar R. ChemPhysChem, 2016, 17, 1-10. (Link)

2015

A Compact Molecule for Redirecting Amyloid-ß Peptides into Nontoxic, Off-pathway Aggregates. Younwoo Nam, Richard A. Kerr, Jeffrey S. Derrick, Hyuck Jin Lee, Kristy L. Peck, Mehmet Ozbil, Kyle J. Korshavn, Ayyalusamy Ramamoorthy, Rajeev Prabhakar, Jason Shearer, Brandon T. Ruotolo, Mi Hee Lim. , Journal of American Chemical Society, 2015, 137 (46), 14785–14797. (Link)

An Extended Polyanion Activation Surface in Insulin Degrading Enzyme. Eun Suk Song, Mehmet Ozbil, Tingting Zhang, Michael Sheetz, David Lee, Danny Tran, Sheng Li, Rajeev Prabhakar, Louis B. Hersh and David W. Rodgers. PLOS ONE, 2015, 10(7): e0133114. (Link)

Hybrid peptide ATCUN-sh-Buforin: Influence of the ATCUN charge and stereochemistry on antimicrobial activity. M. Daben Libardo, Thomas J. Paul, Rajeev Prabhakar, Alfredo Angeles-Boza. Biochimie, 2015, 113, 143-155.  (Link) 

Theoretical Insights into the Functioning of Metallopeptidases and Their Synthetic Analogues. Tingting Zhang, Mehmet Ozbil, Arghya Barman, Thomas J. Paul, Ram Prasad Bora, and Rajeev Prabhakar. Accounts of Chemical Research, 2015, 48(2), 192-200. (Link) 

2014

Role of hydrogen bonds in molecular packing of photoreactive crystals: templating photodimerization of protonated stilbazoles in crystalline state with a combination of water molecules and chloride ions. Barnali Mondal, Tingting Zhang, Rajeev Prabhakar, Burjor Captain and V. Ramamurthy. Photochemical & Photobiological Sciences, 2014, 13, 1509-1520. (Link) 

Computational Insights into Substrate and Site Specificities, Catalytic Mechanism and Protonation States of the Catalytic Asp Dyad of ß-Secretase (BACE1). Arghya Barman and Rajeev  Prabhakar. Scientifica, 2014, doi:10.1155/2014/598728  (Link)

Peptide Hydrolysis by Metal-Cyclen Complexes and Their Analogues: Insights from Theoretical Studies. Tingting Zhang, Xiaoxia Zhu, Rajeev Prabhakar. Organometallics, 2014, 33(8), 1925–1935. (Link) 

Mechanistic Insights into Metal (Pd2+, Co2+ and Zn2+) - Beta Cyclodextrin Catalyzed Peptide Hydrolysis: A QM/MM Approach. Tingting Zhang, Xiaoxia Zhu, Rajeev Prabhakar. Journal of Physical Chemistry B, 2014, 118(15), 4106–4114. (Link)

2013

Pb(II)-promoted Amide Cleavage: Mechanistic Comparison to a Zn(II) Analog. Eric S. Elton, Tingting Zhang, Rajeev Prabhakar, Atta M. Arif, and Lisa M. Berreau. Inorganic Chemistry, 2013, 52(19), 11480-11492.(Link) 

Unraveling the Photoluminescence Response of Light-Switching Ruthenium(II) Complexes Bound to Amyloid-β. Nathan Cook, Mehmet Ozbil, Christina Katsampes, Rajeev Prabhakar, Angel Martí. Journal of American Chemical Society, 2013, 135(29), 10810-10816.(Link)* Highlighted in Chemical and Engineering News & Rice university News and Media & e-Veritas

Elucidating the Catalytic Mechanism of β-secretase (BACE1): A Quantum Mechanics/Molecular Mechanics (QM/MM) Approach. Arghya Barman and Rajeev Prabhakar. Journal of Molecular Graphics and Modelling, 2013, 40, 1-9.(Link)

Experimental and Computational Evidence of Metal-O2 Activation in a Copper Amine Oxidase. Yi Liu, Arnab Mukherjee, Nadav Nahumi, Mehmet Ozbil, Doreen Brown, Alfredo M. Angeles-Boza, David M. Dooley,  Rajeev Prabhakar, and Justine P. Roth. Journal of Physical Chemistry B, 2013, 117(1), 218-229.(Link)

Hydrocarbons Depending on the Chain Length and Head Group Adopt Different Conformations Within a Water-soluble Nanocapsule: 1H NMR and Molecular Dynamics Studies. Rajib Choudhury, Arghya Barman, Rajeev Prabhakar and V. Ramamurthy. Journal of Physical Chemistry B, 2013, 117(1), 398-407.(Link)