About

Shishir Chundawat is an Associate Professor in the Department of Chemical and Biochemical Engineering at Rutgers University, with a tenure appointment since 2021. His research expertise encompasses biochemical engineering, biomanufacturing, biomass process engineering, biopharmaceuticals, bioseparations, carbohydrate-active enzymes (CAZymes), cellulose and carbohydrate chemistry, cellulosic biofuels, chemo-enzymatic synthesis, glycans, and glycoconjugates. He has held various academic and research positions, including Assistant Professor at Rutgers from 2015 to 2021, Assistant Scientist at the Wisconsin Energy Institute, and adjunct/research assistant professor at Michigan State University. His educational background includes a Ph.D. in Chemical Engineering from Michigan State University and a B.Tech. in Chemical Technology from the Institute of Chemical Technology in Mumbai. Dr. Chundawat has received numerous honors, such as the NSF CAREER Award in 2019, the Agilent Faculty Award in 2020, and teaching awards in 2017. His professional experience spans over a decade of research and teaching in chemical and biochemical engineering, with a focus on sustainable biomass conversion, biofuels, and bioprocessing technologies.

Research topics

• Pulp and paper industry
• Organic chemistry
• Computer Science
• Chemistry
• Biotechnology
• Engineering
• Manufacturing engineering
• Waste management
• Biology
• Risk analysis (engineering)
• Agronomy
• Biochemistry
• Operations management
• Business
• Biochemical engineering

Selected publications

• Rafts of change: microbial and functional dynamics in simulated <i>Sargassum</i> strandings

  Applied and Environmental Microbiology · 2026-03-31

  articleOpen access

  ABSTRACT Massive influxes of pelagic Sargassum spp. across the tropical Atlantic and Caribbean regions have created urgent ecological and economic challenges that need to be addressed to stabilize local ecosystems. Use of this abundant biomass feedstock resource for biorefining and bioproducts manufacturing is a promising avenue, but this goal requires elucidating the microbial processes that regulate Sargassum degradation, which are still poorly understood. Here, we investigated the microbial degradation of the benthic Sargassum filipendula by native microbiota using multi-omics approaches. Metagenomic and meta-transcriptomic analyses identified diverse carbohydrate-active enzymes (CAZymes), including alginate lyases, fucoidanases, and cellulases, that were differentially expressed over the course of the in vitro degradation timeline. Furthermore, we identified the need for arsenic detoxification pathways in microbes utilizing Sargassum -derived substrates. We observed a suite of factors influencing microbial dynamics, including prokaryotic competition, arsenic detoxification, viruses, and substrate availability. Lineages potentially capable of degrading recalcitrant polysaccharides such as fucoidan appeared to be rapidly outcompeted by other bacteria that utilized simpler substrates like mannitol. These results highlight the metabolic potential of native marine microbial communities to degrade complex Sargassum polysaccharides and the importance of the in vitro degradation experiment time scale to capture the activities of non-dominant specialists. Our findings elucidate microbial ecosystem dynamics during Sargassum degradation and provide novel insights that can be used to advance the development of biotechnological approaches that leverage renewable Sargassum biomass as a biorefinery feedstock of the future. IMPORTANCE This work addresses a crisis in the tropical Atlantic and Caribbean regions, the massive population growth and stranding of the floating brown seaweed Sargassum , which is wreaking havoc on ecosystems and fouling beaches vital to local tourism. One solution to this problem is to utilize the seaweed as feedstock to generate useful bioproducts. This approach requires characterizing the microbiome of Sargassum that drives its degradation in nature. To this end, we devised an in-lab degradation assay using Sargassum and identified a variety of carbohydrate-active enzymes, including alginate lyases, fucoidanases, and cellulases which break down seaweed cell wall polysaccharides. We also find that microbes compete in the closed reactors, with diversity being reduced over time. These results highlight the metabolic potential of native marine microbial communities to degrade Sargassum and elucidate microbial ecosystem dynamics during this process. These insights allow the use of renewable Sargassum as a biorefinery feedstock of the future.

  PublisherDOI

• There is an “I” in team: individual improvements in supercharged cellulase cocktail facilitates cooperative cellulose degradation

  Biotechnology for Biofuels and Bioproducts · 2026-01-24

  articleOpen accessSenior author

  Lignocellulosic biomass is an abundant renewable carbon source for biofuel production, but its conversion to fermentable sugars is hindered by poor cellulase activity on highly crystalline and insoluble cellulose. While pretreatment makes biomass more amenable to enzymatic degradation, several issues linger related to productive enzyme binding and efficient catalytic turnover. To address this bottleneck, we employed protein supercharging to rationally design a glycosyl hydrolase (GH) family-6 exocellulase (Cel6B) and its native family-2a carbohydrate binding module (CBM2a) from the thermophilic cellulolytic microbe Thermobifida fusca. A chimeric library of 32 supercharged constructs rationally designed across both GH/CBM domains was synthesized and expressed in E. coli. Screening of the entire library of supercharged enzymes on several cellulosic substrates identified one key construct, D5 CBM2a-WT Cel6B, containing a positively supercharged CBM2a that showed 2-threefold higher activity on all substrates tested at pH 5.5. Purified enzyme assays confirmed that exocellulases behave quite differently from their endocellulase counterparts when supercharged using similar protocols. Still, the purified D5 CBM2a-WT Cel6B mutant showed a 2.3-fold improvement in specific activity compared to native enzyme on crystalline cellulose. Analysis of melt curves depicts that, while all other constructs tested have one distinct melt peak near the expected CBM melting point, domain melting is decoupled for the D5 CBM2a mutant. This effect reveals an intrinsic melting temperature of the Cel6B CD nearly 18 °C higher than the coupled melting temperature of the full-length enzyme. This unexpected stabilization effect of supercharged CBM2a domain is likely the driving force for activity improvements seen for this exocellulase that is otherwise prone to stalling and denaturation on the cellulose surface during processive catalytic turnover cycles. When combining this supercharged exocellulase construct with its endocellulase counterpart, our results showed that supercharged enzymes, exhibiting the highest activity alone, produced the best synergistic partners. This study highlights another successful implementation of protein supercharging for cellulases and provides another key piece toward building an effective synergistic cellulase cocktail for lignocellulosic biomass deconstruction.

  PublisherDOI

• Evaluating the impact of media and feed combinations on CHO cell culture performance and monoclonal antibody (trastuzumab) production

  Cytotechnology · 2025-01-09 · 9 citations

  articleOpen accessSenior author

  The choice of media and feeds significantly influences the performance of Chinese Hamster Ovary (CHO) mammalian cell cultures in producing desired biologics like monoclonal antibodies (mAb). Sub-optimal nutrient feed/media composition can severely impact cell proliferation and the quality of the final mAb product. For instance, proper protein glycosylation, crucial for mAb stability, safety, and efficacy, heavily relies on cell culture conditions. Currently, starter CHO culture media and daily supplemental feeds used in industrial manufacturing consist of proprietary composition of nutrients critical for mAb production. Standardized optimal media/feed combinations necessary for different cell lines are often lacking, necessitating individualized optimization for each cell line and mAb product. Here, we focused on a CHO-K1 cell line engineered to produce a Trastuzumab biosimilar and evaluated the effects of fourteen commercially relevant basal media and seven feeds on cell culture parameters such as viable cell density, viability, nutrient consumption, metabolite production, mAb titer, and mAb N-glycosylation. Our findings demonstrate clearly that the compositions of the basal medium and feed play a pivotal role in enhancing cell growth and mAb production. This work offers valuable insights into strategies for optimizing feed/media composition for glycosylated monoclonal antibody production using CHO cells. Supplementary Information: The online version contains supplementary material available at 10.1007/s10616-024-00690-7.

  PublisherOA PDFDOI

• Temporal Galactose‐Manganese Feeding in Fed‐Batch and Perfusion Bioreactors Modulates UDP‐Galactose Pools for Enhanced mAb Glycosylation Homogeneity

  Biotechnology and Bioengineering · 2025-04-18 · 3 citations

  articleOpen accessSenior authorCorresponding

  Monoclonal antibodies (mAbs) represent a majority of biotherapeutics in the market today. These glycoproteins undergo posttranslational modifications, such as N-linked glycosylation, that influence the structural & functional characteristics of the antibody. Glycosylation is a heterogenous posttranslational modification that may influence therapeutic glycoprotein stability and clinical efficacy, which is why it is often considered a critical quality attribute (CQA) of the mAb product. While much is known about the glycosylation pathways of Chinese Hamster Ovary (CHO) cells and how cell culture chemical modifiers may influence the N-glycosylation profile of the final product, this knowledge is often based on the final cumulative glycan profile at the end of the batch process. Building a temporal understanding of N-glycosylation and how mAb glycoform composition responds to real-time changes in the biomanufacturing process will help build integrated process models that may allow for glycosylation control to produce a more homogenous product. Here, we look at the effect of specific nutrient feed media additives (e.g., galactose, manganese) and feeding times on the N-glycosylation pathway to modulate N-glycosylation of a Herceptin biosimilar mAb (i.e., Trastuzumab). We deploy the N-GLYcanyzer process analytical technology (PAT) to monitor glycoforms in near real-time for bench-scale bioprocesses operated in both fed-batch and perfusion modes to build an understanding of how temporal changes in mAb N-glycosylation are dependent on specific media additives. We find that Trastuzumab terminal galactosylation is sensitive to media feeding times and intracellular nucleotide sugar pools. Temporal analysis reveals an increased desirable production of single and double galactose-occupied glycoforms over time under glucose-starved fed-batch cultures. Comparable galactosylation profiles were also observed between fed-batch (nutrient-limited) and perfusion (non-nutrient-limited) bioprocess conditions. In summary, our results demonstrate the utility of real-time monitoring of mAb glycoforms and feeding critical cell culture nutrients under fed-batch and perfusion bioprocessing conditions to produce higher-quality biologics.

  PublisherOA PDFDOI

• There is an “I” in team: individual improvements in supercharged cellulase cocktail facilitates cooperative cellulose degradation

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-17

  preprintOpen accessSenior authorCorresponding

  ABSTRACT Lignocellulosic biomass is a vastly abundant renewable carbon source for biofuel production but its conversion to fermentable sugars is significantly hindered by an inherent recalcitrance to enzymatic degradation. Pretreatment technologies are successful in alleviating some challenges related to substrate recalcitrance, yet enzymes like cellulases still exhibit poor activity on highly crystalline and insoluble cellulose. Both cellulose and lignin present several issues with productive enzyme binding and efficient catalytic turnover. To address these bottlenecks, we employed protein supercharging to rationally design a glycosyl hydrolase (GH) family-6 exocellulase (Cel6B) and its native fused family-2a carbohydrate binding module (CBM2a) from the thermophilic cellulolytic microbe Thermobifida fusca . A total of 16 supercharged variants were designed across both GH/CBM domains and a chimeric library of 32 constructs, including the native enzyme, were synthesized and expressed in E. coli . The entire library of supercharged enzymes was tested for activity on several cellulosic substrates to identify one key construct, D5 CBM2a – WT Cel6B, that had a positively supercharged CBM2a that showed 2-3-fold higher activity on all substrates tested at pH 5.5. Purified enzyme assays confirmed that exocellulases behave quite different from their endocellulase counterparts when supercharged using similar protocols. Still, the purified D5 CBM2a – WT Cel6B mutant showed a 2.3-fold improvement in specific activity compared to native enzyme on crystalline cellulose. Analysis of melt curves depict that, while all other constructs tested have one distinct melt peak near the expected CBM melting point, domain melting is decoupled for the D5 CBM2a mutant. This effect reveals an intrinsic melting temperature of the Cel6B CD nearly 18 °C higher than the coupled melting temperature of the full-length enzyme. This unexpected catalytic domain stabilization effect of supercharged CBM2a domain is likely the driving force for activity improvements seen for this exocellulase that is otherwise prone to stalling and denaturation on the cellulose surface during processive catalytic turnover cycles. When combining this supercharged exocellulase construct with its endocellulase counterpart, our results show that supercharged enzymes that show the highest activity alone, produced the best synergistic partners. This study highlights another successful implementation of protein supercharging strategy for cellulases and provides another key piece towards building an effective synergistic cellulase cocktail for lignocellulosic biomass deconstruction.

  PublisherOA PDFDOI

• Reaction kinetics of procainamide dye derivatization of N-linked glycans to enable robust process analytical workflows for glycoprotein-based biologics manufacturing

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-15

  preprintOpen accessSenior authorCorresponding

  Abstract N-glycosylation is a post-translational modification of proteins that represents a critical quality attribute (CQA) for therapeutics like monoclonal antibodies (mAbs), directly affecting drug efficacy, safety, and stability. Real-time CQA monitoring analytical platforms depend on rapid N-glycan release and fluorophore labeling chemistries to support automated bioprocess analytics during mAb manufacturing. Procainamide is a well-known fluorophore used for released N-glycans reducing sugar aldehydes labeling that offers both high fluorescence and mass spectrometry detection sensitivity comparable to several commercial reagents available in the market. However, currently there are no studies that optimize its use and long incubation times are often reported in the literature for procainamide labeling of N-glycans that has limited its use in time-sensitive workflows relevant to various stakeholders in industry, academia, and regulatory agencies. Here, we have systematically determined the combined procainamide labeling via reductive amination/reduction reaction kinetics at various incubation intervals, ranging from 1 min to 12 h, using N-glycans isolated from model biologic glycoprotein trastuzumab (TmAb). Labeling efficiencies were quantified using high-performance liquid chromatography with fluorescence detection (HPLC-FLR), and detailed reaction parameters were determined by fitting suitable kinetic models. Results indicate that most N-glycans reached over 95% labeling efficiency within 1 hour at the desired reaction temperature. Interestingly, N-glycan structural features, particularly galactosylation and fucosylation levels, significantly influenced the labeling reaction rate. Fucosylated glycans exhibited up to 4-fold higher reaction rate constants than non-fucosylated forms, whereas increased galactosylation levels was associated with slower reaction rate. These results provide essential kinetic benchmarks for incorporating procainamide labeling for released N-glycans, and facilitating more efficient analytical workflows for Process Analytical Technology (PAT) focused on biologics N-glycan analysis in both research and industrial settings.

  PublisherOA PDFDOI

• Time-resolved tracking of cellulose biosynthesis and assembly during cell wall regeneration in live <i>Arabidopsis</i> protoplasts

  Science Advances · 2025-03-21 · 5 citations

  articleOpen accessCorresponding

  Cellulose, the most abundant polysaccharide on earth composing plant cell walls, is synthesized by coordinated action of multiple enzymes in cellulose synthase complexes embedded within the plasma membrane. Multiple chains of cellulose fibrils form intertwined extracellular matrix networks. It remains largely unknown how newly synthesized cellulose is assembled into an intricate fibril network on cell surfaces. Here, we have established an in vivo time-resolved imaging platform to continuously visualize cellulose biosynthesis and fibril network assembly on Arabidopsis thaliana protoplast surfaces as the primary cell wall regenerates. Our observations provide the basis for a model of cellulose fibril network development in protoplasts driven by an interplay of multiscale dynamics that includes rapid diffusion and coalescence of nascent cellulose fibrils, processive elongation of single fibrils, and cellulose fibrillar network rearrangement during maturation. This study provides fresh insights into the dynamic and mechanistic aspects of cell wall synthesis at the single-cell level.

  PublisherOA PDFDOI

• Visualization of Tethered Particle Motion with a Multidimensional Simulation

  The Biophysicist · 2024-01-12

  articleOpen accessSenior author

  ABSTRACT The analysis of particles bound to surfaces by tethers can facilitate understanding of biophysical phenomena (e.g., DNA–protein or protein–ligand interactions and DNA extensibility). Modeling such systems theoretically aids in understanding experimentally observed motions, and the limitations of such models can provide insight into modeling complex systems. The simulation of tethered particle motion (TPM) allows for analysis of complex behaviors exhibited by such systems; however, this type of experiment is rarely taught in undergraduate science classes. We have developed a MATLAB simulation package intended to be used in academic contexts to concisely model and graphically represent the behavior of different tether–particle systems. We show how analysis of the simulation results can be used in biophysical research using single-molecule force spectroscopy (SMFS). Students in physics, engineering, and chemistry will be able to make connections with principles embedded in the field of study and understand how those principles can be used to create meaningful conclusions in a multidisciplinary context. The simulation package can model any given tether–particle system and allows the user to generate a parameter space with static and dynamic model components. Our simulation was successfully able to recreate generally observed experimental trends by using acoustic force spectroscopy (AFS). Further, the simulation was validated through consideration of the conservation of energy of the tether–bead system, trend analyses, and comparison of particle positional data from actual TPM in silico experiments conducted to simulate data with a parameter space similar to the AFS experimental setup. Overall, our TPM simulator and graphical user interface is primarily for demonstrating behaviors characteristic to TPM in a classroom setting but can serve as a template for researchers to set up TPM simulations to mimic a specific SMFS experimental setup.

  PublisherOA PDFDOI

• Acoustic force spectroscopy reveals subtle differences in interfacial protein-polysaccharide binding interactions

  Biophysical Journal · 2024-02-01 · 1 citations

  articleOpen access1st authorCorresponding
  PublisherOA PDFDOI

• Supercharged cellulases show superior thermal stability and enhanced activity towards pretreated biomass and cellulose

  Frontiers in Energy Research · 2024-07-01 · 3 citations

  articleOpen accessSenior authorCorresponding

  Non-productive binding of cellulolytic enzymes to various plant cell wall components, such as lignin and cellulose, necessitates high enzyme loadings to achieve efficient conversion of pretreated lignocellulosic biomass to fermentable sugars. Protein supercharging was previously employed as one of the strategies to reduce non-productive binding to biomass. However, various questions remain unanswered regarding the hydrolysis kinetics of supercharged enzymes towards pretreated biomass substrates and the role played by enzyme interactions with individual cell wall polymers such as cellulose and xylan. In this study, CBM2a (from Thermobifida fusca ) fused with endocellulase Cel5A (from T. fusca ) was used as the model wild-type enzyme and CBM2a was supercharged using Rosetta, to obtain eight variants with net charges spanning −14 to +6. These enzymes were recombinantly expressed in E. coli , purified from cell lysates, and their hydrolytic activities were tested against pretreated biomass substrates (AFEX and EA treated corn stover). Although the wild-type enzyme showed greater activity compared to both negatively and positively supercharged enzymes towards pretreated biomass, thermal denaturation assays identified two negatively supercharged constructs that perform better than the wild-type enzyme (∼3 to 4-fold difference in activity) upon thermal deactivation at higher temperatures. To better understand the causal factor of reduced supercharged enzyme activity towards AFEX corn stover, we performed hydrolysis assays on cellulose-I/xylan/pNPC, lignin inhibition assays, and thermal stability assays. Altogether, these assays showed that the negatively supercharged mutants were highly impacted by reduced activity towards xylan whereas the positively supercharged mutants showed dramatically reduced activity towards cellulose and xylan. It was identified that a combination of impaired cellulose binding and lower thermal stability was the cause of reduced hydrolytic activity of positively supercharged enzyme sub-group. Overall, this study demonstrated a systematic approach to investigate the behavior of supercharged enzymes and identified supercharged enzyme constructs that show superior activity at elevated temperatures. Future work will address the impact of parameters such as pH, salt concentration, and assay temperature on the hydrolytic activity and thermal stability of supercharged enzymes.

  PublisherOA PDFDOI

Recent grants

• A Multiscale Approach to Characterizing Interfacial Carbohydrate-Active Enzymes

  NSF · $559k · 2016–2023

• CAREER: Force spectroscopy enabled multivalent glycan-binding protein engineering

  NSF · $569k · 2019–2026

• SusChEM: Designer Glycoligands for Enabling Targeted Multimodal Protein Bioseparations

  NSF · $300k · 2017–2022

• Collaborative Research: Mechanism-guided enzyme engineering for fucosylated glycoconjugate synthesis

  NSF · $450k · 2019–2024

Frequent coauthors

• Bruce E. Dale

  145 shared

• Venkatesh Balan

  University of Houston

  107 shared

• Leonardo da Costa Sousa

  Michigan State University

  44 shared

• James F. Humpula

  Great Lakes Bioenergy Research Center

  35 shared

• Nirmal Uppugundla

  Michigan State University

  34 shared

• A. Daniel Jones

  Michigan State University

  28 shared

• Dahai Gao

  Beijing Institute of Petrochemical Technology

  28 shared

• Ramin Vismeh

  Biotechnology Institute

  26 shared

Labs

• Chundawat GroupPI

Education

• Ph.D., Chemical Engineering & Materials Science

  Michigan State University

  2009

• B. Tech., Chemical Technology

  Institute of Chemical Technology

  2004

Awards & honors

• Agilent Faculty Award (2020)
• NSF CAREER Award (2019)
• A. Walter Tyson Assistant Professorship Award (2018)
• Undergraduate CBE Teaching Excellence Award (2017)
• Outstanding CBE Faculty Award (2017)