About

Venkata Chirasani is the R. L. Juliano Structural Bioinformatics core director at the UNC School of Medicine, specializing in advanced computational modeling and data analysis to support basic, translational, and clinical research programs. His work focuses on structural bioinformatics, molecular dynamics simulations, protein structure prediction, and AI-assisted drug design, enabling atomic-level understanding of biomolecular systems. He collaborates closely with investigators to design customized computational workflows that complement experimental approaches such as cryo-EM, X-ray crystallography, NMR, and biochemical assays. His research supports a wide range of applications including protein–protein and protein–ligand interaction analysis, structure-based drug discovery, mutation impact assessment, conformational dynamics, and integrative modeling of experimental data. His projects are primarily funded by NIH and foundations, with a focus on cancer biology, cardiovascular disease, neurobiology, ion channel physiology, and genetic disorders. Recent studies include oncogenic RAS signaling, lipid transport mechanisms, ion channel regulation, and therapeutic target identification. In addition to research, he provides training and mentorship in computational biophysics and structural modeling to graduate students, postdoctoral fellows, and faculty, contributing to the interdisciplinary research ecosystem at UNC.

Research topics

• Biology
• Cell biology
• Computer Science
• Chemistry
• Neuroscience
• Biochemistry
• Cancer research
• Nanotechnology
• Immunology
• Materials science
• Genetics

Selected publications

• Characterization of cardiac disease-associated mutations in RyR2 Ca ²⁺ - and caffeine-binding sites

  American Journal of Physiology-Cell Physiology · 2026-02-26

  articleOpen access1st authorCorresponding

  Q3925E in RyR2 is a part of Ca 2+ -binding site and is known to associate with cardiac sudden death. Our functional and structural modeling data suggested that the Q3925E mutation does not reduce Ca 2+ binding but alter a domain interaction, causing an impaired Ca 2+ activation of RyR2. We also found that the Q3925E mutation increases channel inhibition by Mg 2+ and Ca 2+ , resulting in a strong loss-of-function phenotype.

  PublisherOA PDFDOI

• Characterization of cardiac disease-associated mutations in RyR2 Ca2+- and caffeine-binding sites.

  UNC Libraries · 2026-04-10

  articleOpen access1st authorCorresponding

  Cardiac Ca2+ release channels, type-2 ryanodine receptors (RyR2s), play a pivotal role in cardiac muscle contraction by releasing Ca2+ from the sarcoplasmic reticulum. Over 200 missense mutations in humans have been reported to be associated with cardiac diseases. Here, we characterize three RyR2 variants, Q3925E, W4646R, and Q4937K. Q3925E and W4646R mutations are in the Ca2+- and caffeine-binding sites, respectively. Our molecular dynamics simulations predicted that the Q4937 residue in the carboxyl terminal domain forms a hydrogen bond with the central domain where the Ca2+-binding site is located. Three mutant RyR2s were expressed in heterologous cells, and activities of the recombinant mutant RyR2 channels were determined by [3H]ryanodine binding methods. As expected, Q3925E greatly reduced Ca2+-dependent activation and W4646R abolished caffeine activation. Our novel finding is that Q3925E increased inhibitory effects by divalent cations, Ca2+ and Mg2+, resulting in a strong loss-of-function phenotype. Both W4646R and Q4937K increased affinities for Ca2+ activation, and reduced or unchanged Ca2+ inhibitions, exhibiting typical gain-of-function phenotypes. Caffeine failed to activate the Q3925E mutant at resting Ca2+ but restored its activation at ∼20 µM Ca2+, where the Q3925E mutant is in the subactivated state. Computational analysis of the mutated structures suggested that the Q3925E mutation does not reduce Ca2+ binding to its site but rearranges domain interface between the central domain involving Ca2+-binding site and carboxyl terminal domain, which directly interacts with the channel pore. Thus, it is possible that the Q3925E-RyR2 mutation alters signal transmission between activating Ca2+ binding and pore opening.NEW & NOTEWORTHY Q3925E in RyR2 is a part of Ca2+-binding site and is known to associate with cardiac sudden death. Our functional and structural modeling data suggested that the Q3925E mutation does not reduce Ca2+ binding but alter a domain interaction, causing an impaired Ca2+ activation of RyR2. We also found that the Q3925E mutation increases channel inhibition by Mg2+ and Ca2+, resulting in a strong loss-of-function phenotype.

  PublisherDOI

• Histone decrotonylation plays a distinct role in HIV latency

  Science Advances · 2026-04-10

  articleOpen access

  The role of epigenetic regulation in HIV latency remains incompletely understood. We show that histone deacetylase 3 (HDAC3) inhibits trans-activator of transcription (Tat)-mediated HIV transcription through histone decrotonylation (HDCR), independent of deacetylase activity. Chemical biology approaches identified selective HDCR inhibitors (HDCRis) that reverse HIV latency with minimal impact on other histone acylations. Although HDAC2, HDAC3, and HDAC8 exhibit HDCR activity, genetic and chemical studies reveal that the HDCRi citarinostat is selective for HDAC3 and HDAC8. Molecular docking suggests that HDCRi binds outside the zinc-binding pocket, distinct from the classical HDAC inhibitor vorinostat (SAHA, suberoylanilide hydroxamic acid). Key residues (arginine-265, arginine-301, glutamine-113, and aspartic acid–57) are essential for HDCR selectivity, as their mutation abolishes HDCR activity and increases histone crotonylation without altering other acylation marks. Citarinostat increases histone crotonylation at the HIV long terminal repeat, robustly activating HIV transcription in cell lines, primary CD4 + T cells, and brain microglia from simian immunodeficiency virus–infected nonhuman primates and participants enrolled in the Last Gift rapid research autopsy cohort, highlighting HDCR as a promising therapeutic target for HIV latency.

  PublisherDOI

• Functions of the Bloom syndrome helicase N-terminal intrinsically disordered region

  Genetics · 2025-01-10 · 2 citations

  articleOpen access

  Bloom syndrome helicase (Blm) is a RecQ family helicase involved in DNA repair, cell cycle progression, and development. Pathogenic variants in human BLM cause the autosomal recessive disorder Bloom Syndrome, characterized by predisposition to numerous types of cancer. Prior studies of Drosophila Blm mutants lacking helicase activity or protein have shown sensitivity to DNA damaging agents, defects in repairing DNA double-strand breaks (DSBs), female sterility, and improper segregation of chromosomes in meiosis. Blm orthologs have a well-conserved and highly structured RecQ helicase domain, but more than half of the protein, particularly in the N-terminus, is predicted to be intrinsically disordered. Because this region is poorly conserved across metazoa, we compared closely related species to identify regions of conservation that might be associated with important functions. We deleted 2 Drosophila-conserved regions in Drosophila melanogaster using CRISPR/Cas9 gene editing and assessed the effects on several Blm functions. Each deletion had distinct effects. Deletion of either conserved region 1 (CR1) or CR2 compromised DSB repair through synthesis-dependent strand annealing and resulted in increased mitotic crossovers. In contrast, CR2 is critical for embryonic development, but CR1 is less important. Loss of CR1 leads to defects in meiotic crossover designation and patterning but does not impact meiotic chromosome segregation, whereas deletion of CR2 does not result in significant meiotic defects. Thus, while the 2 regions have overlapping functions, there are distinct roles facilitated by each. These results provide novel insights into functions of the N-terminal region of Blm helicase.

  PublisherOA PDFDOI

• Abstract 6944: Transient pan-RAF inhibitor treatment for melanoma prevention

  Cancer Research · 2025-04-21

  article

  Abstract Therapeutic options are currently limited for the 15-25% of cutaneous melanomas driven by an oncogenic NRAS mutation. Our previous findings showed that melanoma-associated NRAS substitutions stabilize conformations optimal for BRAF binding, thereby promoting RAF dimerization, proliferative signaling, and ultimately melanomagenesis. Building on these discoveries, we hypothesized that NRAS-mutant melanoma precursors would exhibit substitution-specific sensitivity to pan-RAF inhibition, and that a temporary blockade of RAF signaling would eliminate NRAS mutant-melanocytes in the skin. BRET and NanoBiT complementation assays revealed that pan-RAF inhibitors promote RAS-RAF and RAF-RAF interactions at lower doses in human melanoma cell lines with a weakly melanomagenic NRAS substitution (Q61H) compared to those with a stronger melanomagenic NRAS substitution (Q61R). Surprisingly, these drug-induced RAF complexes were associated with decreased MAPK>ERK signaling and higher drug sensitivity, suggesting that fully inhibited, drug-bound protomers drive increases in NRAS-RAF interactions. To test the mutation-specific sensitivity of NRAS-mutant melanoma precursors in vivo, mouse models of spontaneous NRAS Q61R- or Q61H-driven melanoma were prophylactically treated with a pan-RAF inhibitor for three days and then followed for tumor formation. Consistent with our in vitro data, short-term pan-RAF inhibitor treatment delayed melanoma onset in NRAS Q61H, but not Q61R mice. These findings highlight the critical role of RAF signaling in NRAS-mutant melanoma formation, suggesting that short-term use of effective, targeted therapies could prevent melanoma formation. Citation Format: Rachel E. Lew, Harsha S. Sanaka, Venkat R. Chirasani, Sharon L. Campbell, Christin E. Burd. Transient pan-RAF inhibitor treatment for melanoma prevention [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6944.

  PublisherDOI

• Allosteric Modulation of Cannabinoid Type 1 Receptor by ZCZ011: Integration of In Vitro Pharmacology and Molecular Dynamics Simulation

  UNC Libraries · 2025-12-17

  articleOpen access

  Over the years, the cannabinoid type 1 receptor (CB1R) has emerged as a promising therapeutic target for addressing various neurodegenerative diseases including HIV-associated neurocognitive disorders (HAND). However, the therapeutic application of direct CB1R activation is often hindered by undesirable psychoactive side effects. To mitigate this issue, research has focused on utilizing positive allosteric modulators (PAMs) to enhance the CB1R activity indirectly. Preclinical studies have highlighted the efficacy of CB1R PAMs, such as ZCZ011 and GAT211, in mouse models of Huntington’s disease, neuropathic pain, and, more recently, HAND. Building on this evidence, we employed primary frontal cortex neuronal cultures and whole brain microglial cultures to investigate the direct and indirect effects of racemic ZCZ011 against the HIV-1 trans-activator of transcription (Tat)-induced excitotoxicity. In parallel, molecular modeling and molecular dynamics simulations were conducted using the ZCZ011 enantiomers (R)-ZCZ011 and (S)-ZCZ011, to elucidate their binding profiles at CB1R. Our in vitro studies revealed that ZCZ011 demonstrated neuroprotective effects against Tat-induced excitotoxicity in the presence of N-arachidonoylethanolamine (AEA) in a dose-dependent manner. Interestingly, racemic ZCZ011 exhibited neuroprotective properties even in the absence of AEA, deviating from the classical behavior of a true PAM. This prompted further investigation into the binding profiles of the enantiomers. Molecular modeling revealed that (R)-ZCZ011 and (S)-ZCZ011 bind to distinct sites on CB1R, aligning with the binding profiles of other CB1R allosteric modulators, GAT228 and GAT229. Notably, (R)-ZCZ011 exhibited a higher number of hydrogen bonds and both polar and nonpolar interactions with CB1R, enhancing the stabilization of AEA binding to CB1R. In summary, these findings suggest that (R)-ZCZ011 may function as both a PAM and an allosteric agonist, like GAT228, while (S)-ZCZ011 may act as a pure PAM, resembling GAT229. This dual functionality underscores the therapeutic potential of ZCZ011 in modulating CB1R activity for a number of neuroprotective applications.

  PublisherDOI

• Structural modifications to pregnane neurosteroids alter inhibition of LPS/Lipid A binding at the MD-2 activation site within the TLR4 signaling complex

  Frontiers in Immunology · 2025-09-04 · 2 citations

  articleOpen access

  Neurosteroids have emerged as promising candidates for treatment for neuroinflammatory diseases, distinct from their classical GABAergic effects. We previously demonstrated that 3α,5α-THP inhibits binding of the Lipid A moiety of lipopolysaccharide to the Toll-like receptor 4 (TLR4): Myeloid Differentiation factor 2 (MD-2) protein complex with nanomolar affinity, suggesting that this mechanism may underlie its ability to inhibit TLR4 signal activation in macrophages and brain. This study investigates the structure activity relationships (SAR) for this action of pregnane neurosteroids, focusing on their interactions with MD-2. Through a combination of molecular docking, surface plasmon resonance, and molecular dynamics simulations, we evaluated how modifications to the A, C, and D rings of neurosteroids influence their interactions with MD-2, including binding affinity, orientation, and conformation. The data reveal that hydrophobic interactions, particularly involving PHE151, may be key to neurosteroid binding to MD-2, and that D ring modification may alter the competitive inhibition of Lipid A binding and subsequent TLR4 activation by pregnane steroids. Furthermore, the prototypical neurosteroids 3α,5α-THP and progesterone demonstrated deeper MD-2 pocket binding and greater MD-2 stabilization, while SGE 516 induced MD-2 flexibility and weaker competitive inhibition compared to 3α,5α-THP. These insights establish a unique structural and mechanistic basis for the immunomodulatory activity of these neurosteroids and offer a novel conceptual framework for future rational design of therapeutics targeting TLR4-mediated neuroinflammation.

  PublisherOA PDFDOI

• Molecular and functional profiling of Gαi as an intracellular pH sensor

  Nature Communications · 2025-04-11 · 2 citations

  articleOpen access

  Heterotrimeric G proteins (Gα, Gβ and Gγ) act downstream of G-protein-coupled receptors (GPCRs) to mediate signaling pathways that regulate various physiological processes and human disease conditions. While human Gαi and its yeast homolog Gpa1 were previously postulated to function as intracellular pH sensors, the pH-sensing capabilities of Gαi and the underlying mechanism remain to be established. Our research shows that variations in pH significantly affect the structure and stability of Gαi-GDP. Specifically, at the lower end of the physiological pH range, the protein undergoes an order-to-disorder transition due to the loss of electrostatic interactions within the Gαi Switch regions, resulting in a reduction in agonist-mediated Gαi-Gβγ release. Further, we identified key residues within the Gαi Switch regions that form the pH-sensing network. Mutation of these residues in Gαi gives rise to 'low pH mimetics' that abolish pH-dependent thermostability changes and reduce Gαi-Gβγ release. Overall, our findings suggest that pH-sensitive structural changes in Gαi impact the agonist-mediated dissociation of Gβγ, which is essential for proper signaling.

  PublisherDOI

• Structural interactions of ankyrin B with NrCAM and β2 spectrin

  Journal of Biological Chemistry · 2025-10-31 · 1 citations

  articleOpen access1st authorCorresponding

  Ankyrin 2 is a high confidence autism spectrum disorder (ASD) gene encoding the spectrin-actin scaffold protein Ankyrin B (AnkB). The 220 kDa isoform of AnkB has multiple functions including developmental spine pruning through L1 family cell adhesion molecules (L1-CAMs) and class 3 Semaphorins on dendrites of pyramidal neurons to achieve an appropriate excitatory balance in the neocortex. Molecular modeling employing AlphaFold was used to predict the structure and interactions of AnkB with the cytoplasmic domain of neuron-glial related L1-CAM (NrCAM), and with β2-Spectrin. The validity of the models was assessed by analyzing protein-protein interactions by co-immunoprecipitation from HEK293 cell lysates after mutating key residues in AnkB predicted to impair these associations. Results revealed a pocket with critical residues in the AnkB membrane-binding domain that engages NrCAM at the conserved cytoplasmic motif - FIGQY. AlphaFold modeling of the AnkB/β2-Spectrin complex identified key interactions between the AnkB spectrin-binding domain and β2-Spectrin repeats 14 to 15. Selected ASD-linked mutations in AnkB predicted to impact binding to NrCAM or β2-Spectrin were then assayed for protein interactions. Maternally inherited ASD missense mutations AnkB A368G located in the NrCAM binding pocket and AnkB R977Q in the Zu5A subdomain disrupted associations with NrCAM and β2-Spectrin, respectively. Moreover, AnkB A368G impaired the neuronal function of 220 kDal AnkB for Semaphorin 3F-induced spine pruning in mouse cortical neuron cultures. These new findings provide structural insights into the L1-CAM/AnkB complex and the molecular basis of ASD etiology associated with AnkB missense mutations.

  PublisherOA PDFDOI

• Evidence for dual roles of histone H3 lysine 4 in antagonizing Polycomb group function and promoting target gene expression.

  UNC Libraries · 2025-05-20

  articleOpen access1st authorCorresponding

  Tight control over cell identity gene expression is necessary for proper adult form and function. The opposing activities of Polycomb and trithorax complexes determine the on/off state of cell identity genes such as the Hox factors. Polycomb group complexes repress target genes, whereas trithorax group complexes are required for their expression. Although trithorax and its orthologs function as methyltransferases specific to histone H3 lysine 4 (H3K4), there is no direct evidence that H3K4 regulates Polycomb group target genes in vivo. Using histone gene replacement in <em>Drosophila</em>, we provide evidence of two key roles for replication-dependent histone H3.2K4 in Polycomb target gene control. First, we found that H3.2K4 mutants mimic H3.2K4me3 in antagonizing methyltransferase activity of the PRC2 Polycomb group complex. Second, we found that H3.2K4 is also required for proper activation of Polycomb targets. We conclude that H3.2K4 directly regulates Polycomb target gene expression.

  PublisherDOI

Frequent coauthors

• Sanjib Senapati

  Indian Institute of Technology Madras

  96 shared

• Prasanna K.R. Allu

  87 shared

• Nitish R. Mahapatra

  Indian Institute of Technology Madras

  85 shared

• Viswanathan Mohan

  Madras Diabetes Research Foundation

  84 shared

• Madhu Khullar

  84 shared

• Ajit S. Mullasari

  Madras Medical Mission

  84 shared

• Arasambattu Kannan Munirajan

  84 shared

• Malapaka Kiranmayi

  Indian Institute of Technology Madras

  84 shared

Labs

• UNC Department of Biochemistry and BiophysicsPI