Biology subjects

Subramanian, G.

Publications and source records attributed to Subramanian, G..

6 recordsLinked to original sources

bioRxiv2026

A Simple Method to Distinguish Active and Inactive Aptamers by Analyzing the Ruggedness of the Aptamer Free Energy Landscape

Aptamers are structured nucleic acid ligands capable of high affinity, high specificity molecular recognition generated using variations of the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) process. However, SELEX often produces sequences that enrich yet may lack binding efficacy. We propose a measure called the Ruggedness Composite Index (RCI) along with a method for computing it, that can be used to distinguish binding-competent ('active') aptamers from weak or non-binding ('inactive') aptamers. Given a set of aptamers, RCI incorporates information on their fragmentation (landscape partitioning), basin entropy (metastable state distribution), cumulative density irregularity (non-uniform occupancy), and structural energy correlation length (structure-energy coupling scale). We test whether secondary-structure folding energy landscape topology distinguishes active from inactive aptamers using a multiscale level set framework across six datasets. Active aptamers show lower RCI values and occupy smoother, funnel-like conformational spaces, while inactive aptamers show higher RCI values, reflecting fragmented, high-entropy landscapes. By contrast, classical thermodynamic features, such as minimum free energy, show limited discrimination between active and inactive aptamers. In all datasets, sequences that exhibit enrichment which is not monotonic but lack specificity exhibit elevated ruggedness, indicating landscape topology can predict non-specific enrichment. These results indicate that folding landscape organization can be used as a predictor of aptamer activity and establish RCI as a simple, mechanistically interpretable measure for improving candidate prioritization, especially in therapeutic aptamer discovery.

bioinformatics↗

bioRxiv2025

Concurrent presentation of memory-related odors and sounds nullified sleep reactivation benefits

AbstractReactivation of recently acquired memories during sleep supports their longevity. Reactivation can be altered during sleep using odors or sounds through a technique termed targeted memory reactivation (TMR). Here, we attempted to selectively weaken memories by reactivating them together with forgetting instructions. We delivered sounds to reactivate spatial memories and concurrent odors to reactivate instructions. Participants learned about the instructions in a Directed-Forgetting task performed with a list of to-be-remembered and to-be-forgotten words. One odor was linked with instructions to forget, one with instructions to remember, and a third was not assigned any meaning. During a nap, sounds previously linked with object-location learning were simultaneously presented with these odors. Spatial recall was tested after sleep. Sound cues produced a selective recall benefit for weakly encoded memories. However, memory results did not support the prediction that forgetting could be instilled by the concurrent forget odor. An encoding-strength-dependent benefit was largest when sounds were presented together with the odor that lacked assigned meaning, whereas the other two odors both disrupted sound-induced memory reactivation. These two odors were linked with instructions and with multiple learning episodes in the Directed-Forgetting task. Accordingly, we infer that reactivation evoked by the remember and forget odor cues interfered with the reactivation of spatial memories. Odors also induced a prolonged decline in sigma EEG power (12-16 Hz) that continued at least 10 s after odor offset. Overall, these findings highlight the complexity of memory consolidation during sleep when multiple memories and multiple cues are involved.

neuroscience↗

bioRxiv2025

CLM296: a highly selective inhibitor targeting ALDH1A3-driven tumor growth and metastasis in breast cancer

Aldehyde dehydrogenase 1A3 (ALDH1A3) increases tumor growth, metastasis, and chemoresistance in many solid tumors, including triple-negative breast cancer (TNBC), glioblastoma, melanoma, lung, and colon cancers, yet no clinically approved inhibitors exist. Here, we present CLM296, a novel and highly selective ALDH1A3 inhibitor designed to address this unmet need. CLM296 exhibits potent inhibition of ALDH1A3 activity in TNBC cells (half-maximal inhibitory concentration = 2 nM) with no off-target effects on the highly homologous ALDH1A1 isoform. RNA sequencing confirmed its specificity, demonstrating selective suppression of ALDH1A3-regulated gene expression only, and a lack of effect in control cells that have minimal ALDH1A3 expression. Transwell assays showed that CLM296 reduced the increased invasion of cells induced by ALDH1A3. Once daily dosing of 4mg/kg CLM296 in mice specifically reduced ALDH1A3-mediated gene expression in tumors and impeded ALDH1A3-driven tumor growth and lung metastasis in TNBC xenografts. There was no observed toxicity in the mice as evidenced by stable mouse body weights and no significant changes in blood creatinine and ALT levels. Pharmacokinetic studies of CLM296 revealed broad tissue distribution, including tumor, lung, liver, and brain. With oral administration the terminal elimination half-life of CLM296 exceeded 12 hours, resulting in sustained ALDH1A3-inhibiting concentrations beyond 24 hours. Together, these findings establish CLM296 as a potential first-in-class ALDH1A3 inhibitor with high selectivity for ALDH1A3, favorable pharmacokinetics, and a positive preclinical safety profile. CLM296 represents a promising therapeutic candidate to complement standard-of-care treatments in ALDH1A3+ cancers.

cancer biology↗

bioRxiv2019

Reticulocyte Infection Leads to Altered Behaviour, Drug Sensitivity and Host Cell Remodelling by Plasmodium falciparum.

Plasmodia are host-specific, both at the organism and cellular levels. During asexual development, Plasmodium spp. infect cells of erythroid lineage, with an overall propensity towards reticulocytes. This applies to even Plasmodium (P.) falciparum, the most common causative agent of human malaria, implications of which remain unexplored. Herein, for the first time, we characterize the developmental stages and features of P. falciparum cultured in vitro in young reticulocytes (CD71+) in comparison to standard normocyte (CD71-) cultures. We demonstrate that there are notable differences in the patterns of invasion, development and sensitivity to potent antimalarials (such as artemisinin and dihydroartemisinin) for parasites residing in CD71+ reticulocytes. Through a transcriptomic approach, we report that P. falciparum parasites are able to sense the host cell environment, and calibrate their metabolic and host cell remodelling pathways through differential gene expression. These results form an exciting avenue on which hitherto unexplored interactions between Plasmodium spp and different stages of host red blood cells could be investigated in the broader contexts of drug resistance, host tropism and zoonosis. Author SummaryParasites causing malaria infect red blood cells for development and proliferation during asexual development. This asexual erythrocytic stage determines higher parasite densities and eventual disease manifestation. Although the most virulent species of Plasmodium infecting humans known as Plasmodium falciparum is able to infect red blood cells of all ages, these parasites show a preference for younger blood cells. Of note, the biochemical and biophysical properties of young and adult red blood cells vary significantly. Herein, we undertook a comparative profiling of invasion process, parasite development and drug response of Plasmoddium falciparum in two host cells: young red blood cells (reticulocytes) and mature red blood cells (normocytes). We demonstrate that P. falciparum infects human reticulocytes with higher affinity and demonstrate differential sensitivity to drugs such as artemisinin while they reside within reticulocytes. Furthermore, we show that P. falciparum is able to detect differences in host environment and adapt to it by changing the expression of genes required for host cell remodelling.

microbiology↗

bioRxiv2019

Whole Cell Phenotypic Screening Of MMV Pathogen Box identifies Specific Inhibitors of Plasmodium falciparum merozoite maturation and egress.

We report a systematic, cellular phenotype-based antimalarial screening of the MMV Pathogen Box collection, which facilitated the identification of specific blockers of late stage intraerythrocytic Plasmodium falciparum maturation. First, from standard growth inhibition asays, we discovered 62 additional antimalarials (EC50 [≤] 10M) over previously known antimalarial candidates from Pathogen Box. A total of 90 potent molecules (EC50 [≤] 1M) were selected for evaluating their stage-specific effects during the intra-erythrocytic development of P. falciparum. None of these molecules had significant effect on ring-trophozoite transition, 10 molecules inhibited trophozoite-schizont transition, and 21 molecules inhibited schizont-ring transition at 1M. These compounds were further validated in secondary assays by flow cytometry and microscopic imaging of treated cells to prioritize 12 molecules as potent and selective blockers of schizont-ring transition. Seven of these were found to strongly inhibit calcium ionophore induced egress of Toxoplasma gondii, a related apicomplexan parasite, suggesting that the inhibitors may be acting via similar mechanism in the two parasites, which can be further exploited for target identification studies. Two of these molecules, with previously unknown mechanism of action, MMV020670 and MMV026356, were found to induce fragmentation of DNA in developing merozoites. Further mechanistic studies would facilitate therapeutic exploitation of these molecules as broadly active inhibitors targeting development and egress of apicomplexan parasites relevant to human health.

microbiology↗

bioRxiv2017

Authentic Enzyme Intermediates Captured "on-the-fly" by Mix-and-Inject Serial Crystallography

Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases. Here, we demonstrate a general method for capturing enzyme catalysis in-action by mix-and-inject serial crystallography. Specifically, we follow the catalytic reaction of the Mycobacterium tuberculosis -lactamase with the 3rd generation antibiotic ceftriaxone by time-resolved serial femtosecond crystallography. The results reveal, in near atomic detail, antibiotic cleavage and inactivation on the millisecond to second time scales including the crossover from transition state kinetics to steady-state kinetics.\n\nSynopsisAn enzymatically catalyzed reaction is initiated by diffusion based mixing of substrate and followed at runtime by time-resolved serial crystallography using a free electron laser.

biophysics↗