Potassium-doped amino acid-rich carbon dots for real-time detection of methotrexate: a novel PL enhancement-based point-of-care sensor Anisha Mandal, Subrahmanyam Sappati, Rahulvarma Katari, Maciej Baginski, Swambabu Varanasi Discover Materials, 2026 Narrow therapeutic index (NTI) drugs are critical for managing serious conditions, but demand constant monitoring due to their narrow margin and risk of inducing nutrient deficiencies. Methotrexate (MTX), for instance, can deplete folate and induce hypokalemia, leading to complications if unmonitored. Photoluminescence (PL)-based sensors offer real-time monitoring potential, yet existing PL quenching models face poor LOD, low linearity, and photo-bleaching. This manuscript aims to develop a sensitive and reliable PL-based sensing strategy that overcomes these limitations by leveraging MTX-induced potassium deficiency to enhance PL response through stable complex formation. To achieve this, potassium-doped, carboxylic- and amide-rich carbon dots (CDs) were synthesized using amino acid-rich palm wine, offering a unique, unexplored approach. These CDs form a stable complex with MTX, resulting in PL enhancement. DFT simulations and comprehensive analyses were performed to delineate the PL enhancement mechanism and evaluate the sensing performance. The synthesized CDs exhibited excellent sensitivity towards MTX, showing a strong linear relationship over a wide concentration range of 1-3000 ppb, and a low LOD of 1.16 ppb (2.55 nM). The selectivity and interference studies confirmed the sensing probes’ robustness in complex environments. The sensing probe quantified MTX in pharmaceutical tablets and cancer patients’ plasma with excellent accuracy. A smartphone-assisted point-of-care (POC) device integrated with the probe demonstrated remarkable performance and suitability in resource-limited settings. This study introduces a CD-based sensing platform in which potassium-doped surface chemistry and CD-MTX complexation enable sensitive, selective, and real-time MTX detection. This CD-based sensor strategy, leveraging NTI-induced deficiencies is extendable to other NTI drugs, as demonstrated herein.
Reactive Glass–Metal Interaction under Ambient Conditions Enables Surface Modification of Gold Nano-Islands Sinorul Haque, Shweta R. Keshri, Ganesh Gadudhula, Kaustuv Chatterjee, Shubhangi Majumdar, Kartick Biswas, Sudheer Ganisetti, Indrajeet Mandal, Dudekula Althaf Basha, Prabir Pal, Pramit K. Chowdhury, Niharika Joshi, Subrahmanyam Sappati, Nitya Nand Gosvami, Pavan Nukala, Eswaraiah Varrla, N. M. Anoop Krishnan, Amarnath R. Allu Advanced Functional Materials, 2026 Stabilizing gold nanoparticles with tunable surface composition via reactive metal–support interactions under ambient conditions remains a formidable challenge. Here, reactive glass–metal interaction (RGMI) is demonstrated as an effective strategy for engineering gold nano‐islands (GNIs) with enhanced stability and tailored surface chemistry. By manipulating sodium aluminophosphosilicate (NAPS) glass composition, it is shown that glass chemistry directly modulates interfacial phenomena, enabling gold nanostructure stability at moderate temperatures (550 °C) in ambient conditions. Comprehensive characterization reveals that adsorption and intercalation of Na and P at GNI surfaces induce lattice distortions in the Au(111) planes and create new electronic states near the Fermi level. This approach bypasses requirements for chemical precursors, reducing agents, extreme temperatures, and extended reaction times, offering an environmentally sustainable fabrication pathway. The resulting GNI–glass interface significantly influences hot carrier dynamics, extending electron lifetimes essential for enhanced catalytic performance. RGMI provides a versatile strategy for engineering stable, multi‐element nanostructures with broad applications in heterogeneous catalysis, sensing, and optoelectronics.
Unraveling the mechanism of graphene oxide-mediated disruption of protein dimers Jyoti Vishwakarma, Dineshbabu Takkella, Sudhanshu Sharma, Abhinav Srivastava, Jacek Czub, Subrahmanyam Sappati, Kolleboyina Jayaramulu, Krishna Gavvala Nanoscale, 2026 Graphene oxide induces β-lactoglobulin dimer dissociation by preferentially adsorbing monomers, as revealed by combined spectroscopy, microscopy, and molecular dynamics simulations, elucidating nanomaterial–protein interface mechanisms.
Bisacridine derivatives as effective eukaryotic topoisomerase II inhibitors Kavya Kondaka, Subrahmanyam Sappati, Kamila Rząd, Ewa Paluszkiewicz, Natalia Maciejewska, Maciej Baginski, Iwona Gabriel European Journal of Medicinal Chemistry, 2026 Fungal infections, particularly those caused by Candida species, pose a growing clinical challenge due to the increasing resistance to conventional antifungal agents and, in general, the limited arsenal of such drugs. In this study, we synthesized and tested a series of novel derivatives of bisacridines as potential antifungal compounds targeting fungal topoisomerase II. These compounds were evaluated for their ability to inhibit yeast topoisomerase II, their antifungal activity, and their selectivity over the human enzyme. Enzymatic assays confirmed that among them, compound IKE16 exhibited a high level of yeast topoisomerase II inhibition with greater selectivity over its human counterpart, as well as a moderate antifungal activity in vitro. Based on in silico approaches, we propose mechanism for this behavior. In particular, molecular docking studies revealed that our compounds exhibit specific "non etoposide-like" type of yeast topoisomerase II inhibition. Moreover, in case of the human enzyme, the compounds are less accommodated to the potential binding sites than in the yeast counterpart. In consequence it may lead to their lower activity against human topoisomerase II. These findings highlight bisacridines as a potential new class of antifungal agents with a novel mechanism of action.
Structural insights into fungal and human topoisomerase II with implications for in silico antifungal drug design Subrahmanyam Sappati, Kavya Kondaka, Iwona Gabriel, Maciej Baginski Scientific Reports, 2025 Topoisomerases are essential enzymes regulating DNA supercoiling and disentanglement, critical for genomic integrity. While topoisomerase inhibitors are well-established in anticancer and antibacterial chemotherapy, their potential as antifungal agents remains underexplored or even not proofed. This study investigates structural distinctions between Saccharomyces cerevisiae topoisomerase II (ScTopoII) and human topoisomerase IIα (hTopoIIα), aiming to identify if ScTopoII can be a selective target for antifungal drug development. A comprehensive sequence analysis, extending to various fungal strains and evolutionary ancient organisms, reveals dissimilarities in the transducer and transducer linker domains of these proteins, as well as in the lysine-rich K-loop region. Molecular dynamics simulations emphasize structural differences in the K-loop, α-helix (or helix-like region), and helix supporting loop region, as well as show unique patterns in hydrophilic and hydrophobic intramolecular interactions in ScTopoII. Moreover, phylogenetic comparisons support the importance of specific regions studied. The study includes topos from different organisms, highlighting discrepancies in helix stability near the K-loop and the role of helix supporting loop region. This broad analysis provides insights into the structural basis of human and fungal enzymes presenting potential pharmacophore “hot spots” in ScTopoII which may give hope for developing selective antifungal agents.
Elucidation of the Synergistic Interaction Between Bilirubin and Casein Protein: An Integrated Spectroscopy and Computational Approach Sudhanshu Sharma, Jyoti Vishwakarma, Jacek Czub, Subrahmanyam Sappati, Krishna Gavvala Biomacromolecules, 2025 High Resolution Image Download MS PowerPoint Slide Herein, we unveil the interaction between bilirubin (BIL), a liver metabolite, and a milk protein, casein (CAS), through an integrated experimental–computational approach. Encapsulation of BIL within CAS protein micelles was characterized by using UV–vis absorption, steady-state fluorescence, and circular dichroism (CD) spectroscopy. CD analysis revealed conformational modulation of BIL upon encapsulation, accompanied by Förster resonance energy transfer (FRET) from CAS’s tryptophans to BIL. 1 H NMR measurements determined specific binding interactions of BIL functional groups involved in micellar interactions, correlating photophysical and electronic properties. The binding affinity of BIL in CAS micelles was found to be on the order of 10 4 M –1 with a spontaneous binding process (−24.56 kJ/mol) driven by entropy gains (467.17 J/mol). TDDFT calculations unveiled red shifts in BIL’s absorption spectra caused by the protein environment. This integrated experimental–computational study provides novel insights into synergetic interactions and structural dynamics between BIL and CAS, shedding light on the influence of milk proteins on bilirubin’s behavior.
Influence of Alcohols on the Bending Rigidity and the Thickness of Phospholipid Membranes: The Role of Chain Length Mismatch Buti Suryabrahmam, Pawel Chodnicki, Subrahmanyam Sappati, Michal Jurkowski, Ayush Agrawal, Jacek Czub, V. A. Raghunathan Journal of Physical Chemistry B, 2025 Alcohols influence the shape of the cells. To elucidate this phenomenon and understand the influence of alcohols on the mechanical properties of cell membranes such as bending rigidity, it is essential to investigate their effects on lipid bilayers. In this study, we explored the impact of short- and medium-chain alcohols on the bending rigidity and thickness of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayers in the fluid phase. We employed various techniques, including vesicle fluctuation analysis, small-angle X-ray scattering, and differential scanning calorimetry. Experimental observations were further validated and interpreted using atomistic molecular dynamics simulations. Our results demonstrate that alcohols ranging from ethanol to octanol reduce the main phase transition temperature (Tm), bending rigidity (κ), and thickness of the bilayer (DHH). Decanol and dodecanol, on the other hand, increase Tm without significantly affecting κ and the bilayer thickness. Our study conclusively shows that alcohols shorter than decanol induce a negative chain length mismatch condition, leading to disorder and enhanced interdigitation in DMPC membranes, resulting in membrane thinning and softening. In contrast, decanol, whose chain length matches that of the lipid, enhances lipid chain order and reduces their interdigitation, resulting in no alteration in the bending rigidity and membrane thickness.
In Silico Functional Annotation and Structural Characterization of Hypothetical Proteins in Bacillus paralicheniformis and Bacillus subtilis Isolated from Honey Ahmer Bin Hafeez, Subrahmanyam Sappati, Radoslaw Krzemieniecki, Randy Worobo, Piotr Szweda ACS Omega, 2025 High Resolution Image Download MS PowerPoint Slide Bacillus species are ubiquitous and survive in competitive microbial communities under adverse environmental conditions. Bacillus paralicheniformis and Bacillus subtilis obtained from honey revealed a significant proportion of proteins within their genomes as uncharacterized hypothetical proteins (HPs). A total of 1007 HP sequences were evaluated, resulting in the successful annotation of 56 HPs by assigning specific functions to them. A systematic in silico approach, integrating a range of bioinformatics tools and databases to annotate functions, characterize physicochemical properties, determine subcellular localization, and study protein–protein interactions, was used. Homology and de novo models were generated for the HPs, coupled with iterative remodeling and molecular dynamics (MD) simulations. HPs having significant roles in sporulation, biofilm formation, motility, ion transportation, regulation of metabolic processes, DNA repair, replication, and transcription were identified. Classical MD simulations of globular and transducer membrane proteins, along with postprocessing analyses, refined our structural predictions and provided deeper insights into the stability and functional dynamics of the protein structures under physiological conditions. Moreover, we observed a correlation between the percentage of α helix, β sheet, and coil structures in globular proteins and transducer membrane proteins. The integration of iterative loop modeling, MD simulations, and Dictionary of Secondary Structure in Proteins analysis further validated our predicted models and facilitated the identification of regions critical for protein function, thereby enhancing the overall reliability and robustness of our functional annotations. Furthermore, annotation of these hypothetical proteins aids in identifying novel proteins within bacterial cells, ultimately contributing to a deeper understanding of bacterial cell biology and their use for biotechnological purposes.
Reactive Glass–Metal Interaction under Ambient Conditions Enables Surface Modification of Gold Nano‐Islands S Haque, SR Keshri, G Gadudhula, K Chatterjee, S Majumdar, K Biswas, ... Advanced Functional Materials 36 (30), e27669 , 2026 2026
Unraveling the Mechanism of Graphene Oxide-Mediated Disruption of Protein Dimers JK Jyothi Vishwakarma, Jacek Czub, Abhinav Srivatsava, Sudhanshu Sharma ... Nanoscale , 2026 2026
Potassium-Doped Amino Acid-Rich Carbon Dots for Real-Time Detection of Methotrexate: A Novel PL Enhancement-Based Point-of-Care Sensor SV Anisha Mandal, Maciej Baginski, Subrahmanyam Sappati Discover Materials , 2026 2026 Citations: 1
Bisacridine derivatives as effective eukaryotic topoisomerase II inhibitors MBIG Kavya Kondaka, Subrahmanyam Sappati, Kamila Rząd, Ewa Paluszkiewicz ... Eur. J. Med. Chem , 2026 2026 Citations: 1
Reactive Glass Metal Interaction under Ambient Conditions Enables Surface Modification of Gold Nanoislands Advanced Functional Materials (10.1002/adfm.202527669) , 2025 2025
Ultrafast Ampipolar Switching in Electrochromic Copolymer Thin Films of Zinc(II) Tetrakis(4-aminophenyl)porphyrin -3,4-ethylenedioxythiophene CK Sachin Kochrekar,* Subrahmanyam Sappati, Plawan Kumar Jha, Ermei Mäkiläe ... Journal of Materials Chemistry C , 2025 2025 Citations: 4
Electronic, magnetic, and mechanical properties of co-doped GaSb: A promising diluted magnetic semiconductor R Samant, D Saraf, RP Adhikari, O Shilkar, S Raikar, A Silveira, M Sawant, ... Journal of Magnetism and Magnetic Materials, 173499 , 2025 2025
Elucidation of Synergistic Interaction Between Bilirubin and Casein Protein: An Integrated Spectroscopy and Computational Approach S Sharma, J Vishwakarma, J Czub, S Sappati, DK Gavvala ACS biomacromolecules , 2025 2025
Influence of Alcohols on the Bending Rigidity and the Thickness of Phospholipid Membranes: The Role of Chain Length Mismatch B Suryabrahmam, P Chodnicki, S Sappati, M Jurkowski, A Agrawal, ... The Journal of Physical Chemistry B 129 (16), 3988-3997 , 2025 2025 Citations: 3
Structural insights into fungal and human topoisomerase II with implications for in silico antifungal drug design MB Subrahmanyam Sappati, Kavya Kondaka, Iwona Gabriel Scientific Reports 15, 9467 , 2025 2025 Citations: 1
In Silico Functional Annotation and Structural Characterization of Hypothetical Proteins in Bacillus paralicheniformis and Bacillus subtilis Isolated from Honey A Bin Hafeez, S Sappati, R Krzemieniecki, R Worobo, P Szweda ACS omega 10 (9), 8993-9006 , 2025 2025 Citations: 2
Pendant Proton‐Relays Systematically Tune the Rate and Selectivity of Electrocatalytic Ammonia Generation in a Fe‐Porphyrin Based Metal–Organic Framework A Ghatak, GS Shanker, S Sappati, I Liberman, R Shimoni, I Hod Angewandte Chemie 136 (37), e202407667 , 2024 2024 Citations: 23
Smartphone-Assisted and Optical Quantification of Copper and Glucose Using Palm Wine-Tailored Carbon Dots and Their Multiple Logic Gate Application A Mandal, S Sappati, A Karmakar, S Pradhan, I Gabriel, S Varanasi ACS Biomaterials Science & Engineering 10 (8), 5362-5380 , 2024 2024 Citations: 4
Why are left-handed G-quadruplexes scarce? M Jurkowski, M Kogut, S Sappati, J Czub The Journal of Physical Chemistry Letters 15 (11), 3142-3148 , 2024 2024 Citations: 3
Low-barrier hydrogen bond determines target-binding affinity and specificity of the antitubercular drug bedaquiline J Słabońska, S Sappati, A Marciniak, J Czub ACS Medicinal Chemistry Letters 15 (2), 265-269 , 2024 2024 Citations: 3
Is protonation of radical anions of 5-bromo-and 5-iodo-4-thio-2’-deoxyuridine in an aqueous solution a primary reason for their different X-ray radiation-induced reactivity? A Szczyrba, S Sappati, M Datta, D Wyrzykowski, S Romanowska, J Czub, ... Doctoral School of Natural Sciences , 2024 2024
Unraveling energy transfer and fluorescence quenching dynamics in biomolecular complexes: a comprehensive study of imiquimod–rifampicin interaction S Sharma, D Takkella, A Srivastava, J Czub, S Sappati, K Gavvala Physical Chemistry Chemical Physics 26 (41), 26291-26303 , 2024 2024 Citations: 6
Initial geometries and MD trajectories of right- and left-handed G-quadruplexes J Jurkowski, M., Kogut, M., Sappati, S., & Czub Chemical sciences (Natural sciences) , 2023 2023
Targeting Spike‐ACE2 Interface of SARS‐CoV‐2 and its Omicron Variant: A Comparative Screening of Potential Inhibitors for Existing and Anticipating Variants Using Molecular … D Takkella, S Sharma, R Krzemieniecki, A Pabbathi, S Sappati, K Gavvala ChemistrySelect 8 (32), e202302687 , 2023 2023 Citations: 4
Reverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants W Ezzemani, A Kettani, S Sappati, K Kondaka, H El Ossmani, ... Journal of Biomolecular Structure and Dynamics 41 (11), 4917-4938 , 2023 2023 Citations: 8
MOST CITED SCHOLAR PUBLICATIONS
Synthesis of Thermally Stable Energetic 1, 2, 3‐Triazole Derivatives AS Kumar, VD Ghule, S Subrahmanyam, AK Sahoo Chemistry–A European Journal 19 (2), 509-518 , 2013 2013 Citations: 80
Understanding the electronic structure and optical properties of vacancy ordered double perovskite A2BX6 for optoelectronic applications M Faizan, X Wang, S Abdelmohsen, KC Bhamu, S Sappati, A Laref, ... ACS Energy & Fuels , 2022 2022 Citations: 63
Nuclear quantum effects in a HIV/cancer inhibitor: The case of ellipticine PG Subrahmanyam Sappati, Ali Hassanali, Ralph Gebauer THE JOURNAL OF CHEMICAL PHYSICS 145 (20), 205102 , 2016 2016 Citations: 44
Ab-initio investigations for structural, mechanical, optoelectronic, and thermoelectric properties of Ba2SbXO6 (XNb, Ta) compounds H Karwasara, KC Bhamu, SG Kang, AK Kushwaha, DP Rai, S Sappati, ... Journal of Alloys and Compounds 893, 162332 , 2022 2022 Citations: 35
Ligand-induced ground-and excited-state chirality in silicon nanoparticles: surface interactions matter M Sujith, EK Vishnu, S Sappati, MS Oliyantakath Hassan, V Vijayan, ... Journal of the American Chemical Society 144 (11), 5074-5086 , 2022 2022 Citations: 34
Surface site modulations by conjugated organic molecules to enhance visible light activity of ZnO nanostructures in photocatalytic water splitting L George, S Sappati, P Ghosh, RN Devi The Journal of Physical Chemistry C 119 (6), 3060-3067 , 2015 2015 Citations: 32
Emergence of aggregation induced emission (AIE), room-temperature phosphorescence (RTP), and multistimuli response from a single organic luminogen by directed structural … A Chatterjee, J Chatterjee, S Sappati, T Sheikh, RM Umesh, MD Ambhore, ... The Journal of Physical Chemistry B 125 (46), 12832-12846 , 2021 2021 Citations: 26
Engineering TADF, mechanochromism, and second harmonic up-conversion properties in regioisomeric substitution space A Chatterjee, J Chatterjee, S Sappati, R Tanwar, MD Ambhore, H Arfin, ... Chemical Science 14 (47), 13832-13841 , 2023 2023 Citations: 25
Pendant Proton‐Relays Systematically Tune the Rate and Selectivity of Electrocatalytic Ammonia Generation in a Fe‐Porphyrin Based Metal–Organic Framework A Ghatak, GS Shanker, S Sappati, I Liberman, R Shimoni, I Hod Angewandte Chemie 136 (37), e202407667 , 2024 2024 Citations: 23
How acidic amino acid residues facilitate DNA target site selection KA Hossain, M Kogut, J Słabońska, S Sappati, M Wieczór, J Czub Proceedings of the National Academy of Sciences 120 (3), e2212501120 , 2023 2023 Citations: 22
Coordination polymers of Fe (III) and Al (III) ions with TCA ligand: Distinctive fluorescence, CO 2 uptake, redox-activity and oxygen evolution reaction B Dhara, S Sappati, SK Singh, S Kurungot, P Ghosh, N Ballav Dalton Transactions 45 (16), 6901-6908 , 2016 2016 Citations: 20
Structural characteristics requisite for the ligand-based selective detection of i-motif DNA S Satpathi, S Sappati, K Das, P Hazra Organic & Biomolecular Chemistry 17 (21), 5392-5399 , 2019 2019 Citations: 16
Spectroscopy and Dynamics of Cryptolepine in the Nanocavity of Cucurbit [7] uril and DNA RK Koninti, S Sappati, S Satpathi, K Gavvala, P Hazra ChemPhysChem 17 (4), 506-515 , 2016 2016 Citations: 16
Mangiferin Affects Melanin Synthesis by an Influence on Tyrosinase: Inhibition, Mechanism of Action and Molecular Docking Studies MBJRO Anna Hering, Justyna Stefanowicz-Hajduk, Szymon Dziomba, Rafal Halasa ... Antioxidants 12 (5), 1016 , 2023 2023 Citations: 15
Anilate tethered neutral tetrahedral Pd (II) cages exhibiting selective encapsulation of xylenes and mesitylene A Yadav, M Sarkar, S Subrahmanyam, A Chaudhary, E Hey‐Hawkins, ... Chemistry–A European Journal 26 (19), 4209-4213 , 2020 2020 Citations: 15
An insight into the mixed quantum mechanical-molecular dynamic simulation of a ZnII-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding … TSSS Saurabh Das International Journal of Biological Macromolecules. , 2023 2023 Citations: 14
Inhibition ability of natural compounds on receptor-binding domain of SARS-CoV2: an in silico approach M Nedyalkova, M Vasighi, S Sappati, A Kumar, S Madurga, V Simeonov Pharmaceuticals 14 (12), 1328 , 2021 2021 Citations: 14
Proton-coupled electron transfer in the aqueous nanochannels of lyotropic liquid crystals: Interplay of H-bonding and polarity effects K Das, S Sappati, GS Bisht, P Hazra The Journal of Physical Chemistry Letters 12 (10), 2651-2659 , 2021 2021 Citations: 9
Sensitizing with short conjugated molecules: Multimodal anchoring on ZnO nanoparticles for enhanced electron transfer characteristics, stability and H2 evolution L George, S Sappati, P Ghosh, RN Devi Catalysis Today 309, 89-97 , 2018 2018 Citations: 9
Reverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants W Ezzemani, A Kettani, S Sappati, K Kondaka, H El Ossmani, ... Journal of Biomolecular Structure and Dynamics 41 (11), 4917-4938 , 2023 2023 Citations: 8
