Biology subjects

Dubovski, N.

Publications and source records attributed to Dubovski, N..

4 recordsLinked to original sources

bioRxiv2026

Dual-Specific Antibody Design Using Artificial Intelligence

Multibodies, or "two-in-one" Immunoglobulin G (IgG) antibodies, are standard symmetrical IgG molecules engineered to competitively bind more than one antigen within a single variable fragment (Fv) binding surface. This format merges the functional advantages of bispecifics, such as multi-target binding and dynamic adaptation to target concentrations, with the superior manufacturing, developability, pharmacokinetics, and avidity of monospecific IgGs. Moreover, the co-accommodation of multiple paratopes on a single set of 6 CDRs introduces new functional possibilities that can improve efficacy and safety. Multibodies can, therefore, be thought of as force multipliers: for any format of antibodies, or fragments thereof, multibodies can bind double the number of epitopes compared to standard antibodies. While these advantages were recognized more than 15 years ago, the systematic design of multibodies has been intractable due to the challenge of optimizing two binding specificities into one Fv region, without having one of them compromising the other and without inducing poly-reactivity. To overcome this engineering barrier, we have developed an artificial intelligence (AI)-assisted computational platform that enables the design of functional multibodies against virtually any pair of targets. We applied the platform to design nine multibodies combining 15 different unrelated targets. We obtained therapeutic-grade multibodies that bind each desired pair of targets. We demonstrate that the generated multibodies possess excellent developability, high affinity, and stringent specificity, comparing favorably to clinical monospecific benchmarks. Critically, we show that these multibodies exhibit superior functional activity across a diverse range of mechanisms of action (MOAs), including internalization, T-cell engagement, and immune system modulation. This capability to reliably engineer versatile multibodies opens a new domain in antibody therapeutics, enabling complex multipharmacology and novel functions within a natural, cost-effective, and highly developable format. Two of these multibodies are currently in IND enabling studies, with first in human studies expected in 2026. The timeline from idea to a fully optimized, developable, lead candidate, ready for IND enabling studies, is 9 months.

bioengineering↗

bioRxiv2022

Sensitivity of human sweet taste receptor subunits T1R2 and T1R3 to activation by glucose enantiomers

We have previously shown that L-glucose, the non-caloric enantiomer of D-glucose, activates the human sweet taste receptor T1R2/T1R3 transiently expressed in HEK293T cells. Here we show that D- and L-glucose can also activate T1R2 and T1R3 expressed without the counterpart monomer. Serine mutation to alanine in residue 147 in the binding site of T1R3 VFT domain, completely abolishes T1R3S147A activation by either L or D-glucose, while T1R2/T1R3S147A responds in the same way as T1R2 expressed without its counterpart. We further show that the original T1R2 reference sequence (NM_152232.1) is less sensitive by almost an order of magnitude than reference sequence at the time this study was performed (NM_152232.4). We find that out of the four differing positions, it is the R317G in the VFT domain of T1R2, that is responsible for this effect in-vitro. It is important both for practical assay sensitivity, and because glycine is found in this position in [~]20% of the world population. While the effects of the mutations and of the partial transfections were similar for D and L enantiomers, their dose response curves remained distinct, with L-glucose reaching an early plateau.

biochemistry↗

bioRxiv2020

Sweet chirality: the taste of L and D glucose stereoisomers

Chirality plays a key role in biomolecular recognition. Typically, a change in chirality will dramatically affect ligand-receptor binding. However, both O_SCPLOWDC_SCPLOW-glucose and its enantiomer O_SCPLOWLC_SCPLOW-glucose elicit sweet taste in humans. We show that O_SCPLOWLC_SCPLOW- and O_SCPLOWDC_SCPLOW-glucose are perceived as similarly sweet by humans, and that in cell-based functional assays, both enantiomers activate the human sweet taste receptor TAS1R2/TAS1R3. We hypothesize that both O_SCPLOWLC_SCPLOW- and O_SCPLOWDC_SCPLOW-glucose occupy the orthosteric binding site in the VFT domain of TAS1R2. Using induced-fit docking to a homology model of this domain, we identify two subpockets in this binding site. The model suggests that glucose molecules can bind in either of these subpockets, which overlap with the predicted positions of monosaccharide units of sucrose. One subpocket is close to the hinge between the two lobes, and overlaps with aspartame and neotame site, the second subpocket overlaps with that described for sweetness enhancers. These findings suggest a framework for rational design of sweeteners combinations.

biochemistry↗

bioRxiv2020

Sweet taste of heavy water

Hydrogen to deuterium isotopic substitution has only a minor effect on physical and chemical properties of water and, as such, is not supposed to influence its neutral taste. Here we conclusively demonstrate that humans are, nevertheless, able to distinguish D2O from H2O by taste. Indeed, highly purified heavy water has a distinctly sweeter taste than same-purity normal water and adds to perceived sweetness of sweeteners. In contrast, mice do not prefer D2O over H2O, indicating that they are not likely to perceive heavy water as sweet. HEK 293T cells transfected with the TAS1R2/TAS1R3 heterodimer and chimeric G-proteins are activated by D2O but not by H2O. Lactisole, which is a known sweetness inhibitor acting via the TAS1R3 monomer of the TAS1R2/TAS1R3, suppresses the sweetness of D2O in human sensory tests, as well as the calcium release elicited by D2O in sweet taste receptor-expressing cells. The present multifaceted experimental study, complemented by homology modelling and molecular dynamics simulations, resolves a long-standing controversy about the taste of heavy water, shows that its sweet taste is mediated by the human TAS1R2/TAS1R3 taste receptor, and opens way to future studies of the detailed mechanism of action. One sentence summaryHeavy water elicits sweet taste for humans via the TAS1R2/TAS1R3 taste receptor.

biochemistry↗