Potential clients include small- and medium-sized pharmaceutical and
biotech companies wishing to utilize specialized, limited-time contract
research and/or consulting relating to protein structure and dynamics.
RECONESIS can provide advice and/or actual computational biology/computational
chemistry research in this area, for a specific period of time, and
with full confidentiality. RECONESIS aims to provide research support
to what could be obtained from a collaboration with an academic basic
science research group. However, such collaborations with academia
often are not possible without sharing intellectual property rights.
RECONESIS will perform research services and consulting for a defined
no claim on intellectual property.
1. Peptide design
Conformational analysis using designed constrained peptides. Conformationally
constrained peptides can be used as probes for receptor-bound conformations
of peptide ligands. This can aid in further optimization of such peptides
as a basis for biologics (protein-based therapeutics) or to create peptide
structural templates for non-peptide drug candidates.
2. Computational chemistry / biology
Practical applications of molecular dynamics simulations
- Enhanced understanding of ligand binding phenomena, protein-protein
interactions, protein stability, and protein aggregation. In particular,
entropic and allosteric effects can be predicted in some cases. This
could be particularly useful in understanding the protein-protein
interactions involved in the activity of biologics such as vaccines
- New approaches to ligand design, such as designing allosteric
inhibitors or activators of proteins. These approaches can be suggested
and planned for application by your company or another lab, or actually
carried out by RECONESIS as contract research.
- New approaches to protein engineering, using amino acid substitutions
to induce and/or alter allosteric pathways.
- Prediction of the effects of disease-related mutations, to
suggest therapeutic approaches that counteract these effects, particularly
using allosteric effects of artificial mutations to predict binding
sites for allosterically-acting drugs.
3. Other support
- Consulting, advice, and assistance in the setup and use of
advanced molecular dynamics techniques in your group.
- Consulting, advice, and assistance in application of other protein
modeling and computational biology techniques.
- Design of transforming growth factor-β mimics (receptor agonists
and antagonists), as described in United States patents US 6,638,912
B2 and US 6,509,318 B1.
on cancer-inducing allosteric effects on protein-protein interactions
in the tumor suppressor BRCA1: Gough, C.A.; Gojobori, T.; and Imanishi,
T. "Cancer-related mutations in BRCA1-BRCT cause long-range structural
changes in protein-protein binding sites: a molecular dynamics study."
(2007). Proteins 66(1): 69-86.
on allosteric phenomena in transthyretin that destablize protein-protein
interactions via entropic effects. Presentation of this work available
on request; publication in preparation: Gough, C.A.; Gojobori, T.;
Imanishi, T. "Dynamic phenomena and amyloidogenicity in transthyretin:
a molecular dynamics study."
- Performed an analysis of medical device clinical studies conducted
by the United States Food and Drug Administration (FDA), in order to
extract the essential factors used in FDA approval of such devices.
This was performed to assist researchers at Tokyo Women's Medical University
in their project to develop standards for approval of such devices by
the Japanese government.