About

Konstantin Popov is an Adjunct Associate Professor in the Department of Biochemistry and Biophysics at the University of North Carolina at Chapel Hill. He is affiliated with the Pharmacy – Division of Chemical Biology and Medicinal Chemistry, and serves as the Director of Pharmacy – Computation Biophysics at the Center for Integrative Chemical Biology and Drug Discovery. His research focuses on biochemistry and biophysics, with an emphasis on computational approaches to chemical biology and drug discovery. He is based at 125 Mason Farm Road, 3205 Marsico Hall, Chapel Hill, NC 27599-7363, and can be contacted via phone at 919-843-8457 or email at kpopov@email.unc.edu.

Research topics

• Chemical engineering
• Materials science
• Chemistry
• Organic chemistry
• Metallurgy
• Physical chemistry
• Inorganic chemistry
• Composite material
• Mineralogy
• Nanotechnology

Selected publications

• Some misconceptions about scale inhibition mechanisms: A review

  Desalination · 2026-04-24

  articleOpen access1st author

  The substoichiometric scale inhibitors are recently broadly applied in desalination plants, boilers, open-circuit water cooling systems, geothermal well systems, oilfield facilities, pulp and paper factories and waste water treatment applications. Numerous attempts are being made worldwide to develop new antiscalants in order to enhance their efficiency and environmental acceptability under assumption, that the mechanisms of action are based on the effects of chelation, dispersion and scale crystals distortion. However, a critical reevaluation of the current understanding of these mechanisms is required, as recent advancements in antiscalant direct visualization, chemical speciation, and in-depth analysis of experimental contradictions suggest a more nuanced perspective. The present review aims to challenge and clarify common misconceptions surrounding the scale inhibition mechanisms, providing a systematic discussion of key findings and proposing innovative alternative approaches for future research in the field. Our goal is to foster a more informed and united research agenda that addresses the complexities and limitations of existing antiscalant technologies, with the ultimate objective of developing more sustainable and effective solutions to the pressing issue of scale formation. • Debunks myths: calcium masking, crystal habit relevance, and zeta-potential impact • Reveals contradictions on assumed vs actual locations of scale inhibitor molecules • Antiscalant visualization and full speciation are vital to grasp activity. • Natural nano/micro-impurities drive inhibition; shift to antiscalant-impurity studies • Shows need to study and control nanoimpurities in labs and field water treatment

  PublisherDOI

• List of contributors

  Elsevier eBooks · 2025-11-29

  book-chapter
  PublisherDOI

• Fluorescent phosphonates for water treatment applications

  Elsevier eBooks · 2025-11-29

  book-chapter1st authorCorresponding
  PublisherDOI

• Self-Employment as a Signal: Career Concerns with Hidden Firm Performance

  SSRN Electronic Journal · 2025-01-01 · 1 citations

  preprintOpen access
  PublisherDOI

• Novel Computational Pipeline to Identify Target Sites for Broad Spectrum Antiviral Drugs

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-30 · 1 citations

  preprintOpen access

  Emerging viruses pose an ongoing threat to human health. While certain viral families are common sources of outbreaks, predicting the specific virus within a family that will cause the next outbreak or pandemic is not possible, creating an urgent need for broad spectrum antiviral drugs that are effective against an array of related viral pathogens. However, broad spectrum drug development is hindered by the lack of detailed knowledge of compound binding sites that are structurally and functionally conserved between viral family members and are essential for virus replication. To overcome this limitation, we developed an in silico approach that combines AI-driven protein structure prediction, computational fragment soaking, multiple sequence alignment, and protein stability calculations to identify highly conserved target sites that are both solvent-accessible and conserved. We applied this approach to the Togaviridae family, which includes emerging pandemic disease threats such as chikungunya and Venezuelan equine encephalitis virus for which there are currently no approved antiviral therapies. Our analysis identified multiple solvent accessible and structurally conserved pockets in the alphavirus non-structural protein 2 (nsP2) protease domain, which is essential for processing of the viral replicase proteins. Mutagenesis of key solvent accessible and conserved residues identified novel pockets that are essential for protease activity and the replication of multiple alphaviruses, validating these pockets as potential antiviral target sites for nsP2 inhibitors. These findings highlight the potential of artificial intelligence-informed modeling for revealing functionally conserved, accessible pockets as a means of identifying potential target binding sites for broadly active direct acting antivirals. Significance Statement: Here we present a novel integrative computational approach to identify novel target sites for broadly acting antiviral drugs. We used this technique to identify multiple functionally and structurally conserved protein surface pockets within the alphavirus nsP2 protease and methyl-transferase-like domain. Mutagenesis of these pockets identified that they are essential for protease activity and replication of a genetically diverse group of alphaviruses, validating these sites as potential targets for broadly active small molecule alphavirus inhibitors. This integrative AI-driven approach thus provides an important tool in developing antivirals essential for pandemic preparedness.

  PublisherOA PDFDOI

• Measurement of Position Resolutions of L-band Cavity Beam Position Monitors

  ArXiv.org · 2025-12-15

  preprintOpen access

  Beam position monitors (BPMs) are indispensable components of modern particle accelerators, providing real-time diagnostics to ensure precise beam control, stability, and quality. As accelerators such as the International Linear Collider (ILC) aim for nanometer-scale beam sizes at the interaction point, stringent requirements on position resolution arise. Specifically, the main linac of the ILC demands a BPM resolution better than 5 μm to support stable beam transport and minimize emittance growth. To address this, we have developed an L-band cavity BPM optimized for the beam conditions of the ILC. In this paper, we introduce a prototype of an L-band cavity BPM and its signal processing system, describe the methodology for position resolution measurements, discuss the problems and solutions encountered in the past experiment, and report the projected position resolutions of about 300 nm at best.

  PublisherOA PDFDOI

• A flexible, allosteric loop regulates protein activity and rewires electrostatics

  Protein Science · 2025-09-24 · 3 citations

  articleOpen access

  Allostery is a key driver of protein function and behavior in biological systems. Historically, allosteric regulation has been attributed to conformational and dynamic changes, mostly derived from well-structured regions of proteins. While the regulatory contributions of specific unstructured elements, such as catalytic loops near the active site, have been widely characterized, the role of distal, flexible loops remains poorly understood. Here, we investigate the allosteric protein chorismate mutase (CM), a homodimeric enzyme critical for the biosynthesis of aromatic amino acids. Although CM is differentially regulated by tryptophan and tyrosine via a shared pocket over 25 Å from the active site, their near-identical NMR spectra suggest that alternative mechanisms may explain TrpCM and TyrCM's distinct functional landscapes. We demonstrate that a mutation within a structurally invisible and highly flexible loop, loop 11-12, located far from the active site, drastically alters CM's activity landscape. Using paramagnetic labeling of the loop, we show that loop 11-12 undergoes transient excursions toward the active site, but only in the presence of the activator Trp, which binds over 20 Å away. Furthermore, employing a novel NMR approach, we show that loop 11-12 modulates CM's electrostatics, potentially influencing charge distribution to provide another control of enzymatic activity. Our findings support a sophisticated allosteric process in which a flexible, distal loop is functionally coupled to both the effector binding region and the active site. This mechanism provides new insights into the diverse ways proteins achieve allosteric regulation and may contribute to understanding flexible regions in other allosteric systems.

  PublisherOA PDFDOI

• Development of Next Generation Cell-Permeable Peptide Inhibitors for the Oncological Target MAGE-A4

  Journal of Medicinal Chemistry · 2025-09-12 · 1 citations

  article

  Melanoma-associated antigen A4 (MAGE-A4) is a cancer/testis antigen (CTA) that interacts with the E3 ubiquitin ligase RAD18 to enhance DNA damage tolerance in tumor cells. Here, we report the structure-guided optimization of a previously reported potent but cell-impermeable cyclic peptide, called MTP-1. Building off our previous peptide inhibitor efforts, we aimed to develop next-generation peptide inhibitors with significantly improved cell permeability. Through systematic structure–activity relationship (SAR) studies employing an mRNA display site-saturation mutagenesis library (SSML) and strategic scaffold optimization with modified cyclization strategy, we developed JWP24, the first cell-permeable peptide inhibitor of MAGE-A4. Evaluation across multiple assays demonstrates intracellular target engagement, maintained binding potency, and exhibits no cytotoxicity at effective concentrations. This study provides a valuable framework for transforming potent but larger, macrocyclic peptide inhibitors into cell-permeable probes. The work presented here demonstrates progress toward further establishing MAGE-A4 as a chemically tractable oncology target.

  PublisherDOI

• Self-Employment as a Signal: Career Concerns with Hidden Firm Performance

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access
  PublisherDOI

• Self-Employment as a Signal: Career Concerns with Hidden Firm Performance

  ArXiv.org · 2025-09-01

  preprintOpen access

  We study a dynamic labor market in which a risk-averse worker with career concerns chooses each period between self-employment, which generates publicly observed binary output, and employment at a firm, which pays a flat wage but keeps individual performance hidden from the outside market. The worker values future opportunities through a reputation for talent, understood as the public belief used by firms to set wages. Firms may be myopic, pricing only off public beliefs, or sophisticated, inferring from who is expected to apply. Three forces organize the results: an insurance - information trade-off, selection by talent, and inference from application decisions. A self-confirming absorbing hidden-employment region arises naturally when the value of insurance dominates the value of additional public signals, so some workers optimally stop generating public information. At any public belief there is a unique talent cutoff governing selection into self-employment, and sophisticated firms, by internalizing application-based inference, compress wages and induce different patterns of public information production than myopic firms. The framework yields testable predictions for the prevalence of self-employment, switching into opaque jobs, and wage dynamics across markets with different degrees of performance transparency.

  PublisherOA PDFDOI

Frequent coauthors

• V. Yu. Bychenkov

  Institute of Applied Physics

  81 shared

• Nebojša D. Nikolić

  University of Belgrade

  64 shared

• Lora Ramunno

  University of Ottawa

  63 shared

• P. V. Nickles

  Max-Born-Institute for Nonlinear Optics and Short Pulse Spectroscopy

  56 shared

• M. Schnürer

  European X-Ray Free-Electron Laser

  49 shared

• S. Steinke

  49 shared

• R. Prasad

  49 shared

• N. V. Zmitrenko

  49 shared

Labs

• UNC Department of Biochemistry and BiophysicsPI

Education

• Chemist, Depatrement of Chemistry

  Moscow State University

  1972